PDB Short entry for 2EC8 HEADER TRANSFERASE 11-FEB-07 2EC8 TITLE CRYSTAL STRUCTURE OF THE EXCTRACELLULAR DOMAIN OF THE RECEPTOR TITLE 2 TYROSINE KINASE, KIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAST/STEM CELL GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAINS, D1-D5; COMPND 5 SYNONYM: SCFR, PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT, C-KIT, COMPND 6 CD117 ANTIGEN; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KIT; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PFASTBAC1 KEYWDS GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, GROWTH FACTOR CYTOKINE, KEYWDS 2 DIMERIZATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YUZAWA,Y.OPATOWSKY,Z.ZHANG,V.MANDIYAN,I.LAX,J.SCHLESSINGER REVDAT 4 29-JUL-20 2EC8 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 2EC8 1 VERSN REVDAT 2 24-FEB-09 2EC8 1 VERSN REVDAT 1 07-AUG-07 2EC8 0 JRNL AUTH S.YUZAWA,Y.OPATOWSKY,Z.ZHANG,V.MANDIYAN,I.LAX,J.SCHLESSINGER JRNL TITL STRUCTURAL BASIS FOR ACTIVATION OF THE RECEPTOR TYROSINE JRNL TITL 2 KINASE KIT BY STEM CELL FACTOR JRNL REF CELL(CAMBRIDGE,MASS.) V. 130 323 2007 JRNL REFN ISSN 0092-8674 JRNL PMID 17662946 JRNL DOI 10.1016/J.CELL.2007.05.055 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12521 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 650 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 853 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3900 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : -0.76000 REMARK 3 B33 (A**2) : 1.14000 REMARK 3 B12 (A**2) : -0.38000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.481 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.464 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 54.785 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.891 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.866 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3658 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5001 ; 1.848 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 6.211 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;36.886 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 520 ;20.571 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;12.511 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2756 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1596 ; 0.303 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2467 ; 0.339 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 137 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 57 ; 0.334 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.357 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2351 ; 2.544 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3709 ; 4.056 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1478 ; 3.596 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1292 ; 5.334 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8110 19.9828 20.6287 REMARK 3 T TENSOR REMARK 3 T11: 0.2454 T22: 0.2149 REMARK 3 T33: 0.2111 T12: -0.0032 REMARK 3 T13: 0.0417 T23: 0.0945 REMARK 3 L TENSOR REMARK 3 L11: 1.3685 L22: 2.4699 REMARK 3 L33: 0.0893 L12: -1.7305 REMARK 3 L13: 0.2285 L23: -0.1689 REMARK 3 S TENSOR REMARK 3 S11: 0.0857 S12: 0.0780 S13: 0.1716 REMARK 3 S21: -0.1564 S22: -0.1629 S23: -0.1522 REMARK 3 S31: 0.0366 S32: 0.0379 S33: 0.0772 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 306 A 433 REMARK 3 ORIGIN FOR THE GROUP (A): -46.9154 76.1123 21.4884 REMARK 3 T TENSOR REMARK 3 T11: 0.2819 T22: 0.3363 REMARK 3 T33: 0.0353 T12: 0.0536 REMARK 3 T13: -0.0172 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.6629 L22: 1.4001 REMARK 3 L33: 0.3672 L12: -0.8148 REMARK 3 L13: 0.7008 L23: -0.6730 REMARK 3 S TENSOR REMARK 3 S11: 0.1410 S12: -0.2771 S13: -0.1299 REMARK 3 S21: -0.1079 S22: -0.0887 S23: 0.0213 REMARK 3 S31: -0.1589 S32: -0.0511 S33: -0.0523 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 434 A 508 REMARK 3 ORIGIN FOR THE GROUP (A): -67.5318 97.8256 35.4108 REMARK 3 T TENSOR REMARK 3 T11: 0.1245 T22: 0.2718 REMARK 3 T33: 0.3668 T12: 0.1940 REMARK 3 T13: 0.0089 T23: 0.1035 REMARK 3 L TENSOR REMARK 3 L11: 10.3495 L22: 3.3222 REMARK 3 L33: 2.0595 L12: -4.1168 REMARK 3 L13: -4.1041 L23: 2.4856 REMARK 3 S TENSOR REMARK 3 S11: 0.6252 S12: 0.5941 S13: 1.4900 REMARK 3 S21: 0.2246 S22: 0.0488 S23: -0.3266 REMARK 3 S31: 0.1811 S32: 0.1402 S33: -0.6740 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2EC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026489. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13342 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 400, 0.2M KCL, 0.1M NA-PI REMARK 280 BUFFER, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 81.12450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.83725 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.52867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 81.12450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 46.83725 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.52867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 81.12450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 46.83725 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.52867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 93.67450 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 45.05733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 93.67450 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 45.05733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 93.67450 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 45.05733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS MONOMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 TRP A 8 REMARK 465 ASP A 9 REMARK 465 PHE A 10 REMARK 465 ARG A 19 REMARK 465 VAL A 20 REMARK 465 GLN A 21 REMARK 465 THR A 22 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 GLN A 26 REMARK 465 PRO A 27 REMARK 465 SER A 28 REMARK 465 VAL A 29 REMARK 465 SER A 30 REMARK 465 PRO A 31 REMARK 465 GLY A 32 REMARK 465 GLN A 190 REMARK 465 GLU A 191 REMARK 465 GLY A 192 REMARK 465 LYS A 193 REMARK 465 PRO A 444 REMARK 465 GLY A 445 REMARK 465 THR A 446 REMARK 465 GLU A 447 REMARK 465 GLN A 448 REMARK 465 ARG A 449 REMARK 465 CYS A 450 REMARK 465 SER A 451 REMARK 465 ALA A 452 REMARK 465 SER A 453 REMARK 465 SER A 465 REMARK 465 ASN A 486 REMARK 465 GLY A 487 REMARK 465 THR A 488 REMARK 465 VAL A 489 REMARK 465 GLU A 490 REMARK 465 LYS A 509 REMARK 465 GLY A 510 REMARK 465 ASN A 511 REMARK 465 ASN A 512 REMARK 465 LYS A 513 REMARK 465 GLU A 514 REMARK 465 GLN A 515 REMARK 465 ILE A 516 REMARK 465 HIS A 517 REMARK 465 PRO A 518 REMARK 465 HIS A 519 REMARK 465 HIS A 520 REMARK 465 HIS A 521 REMARK 465 HIS A 522 REMARK 465 HIS A 523 REMARK 465 HIS A 524 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 11 CG CD1 CD2 REMARK 470 LEU A 18 CG CD1 CD2 REMARK 470 GLU A 33 CG CD OE1 OE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLN A 152 CG CD OE1 NE2 REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 LEU A 156 CG CD1 CD2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 ASP A 159 CG OD1 OD2 REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 163 CG1 CG2 CD1 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 SER A 187 OG REMARK 470 VAL A 188 CG1 CG2 REMARK 470 LEU A 222 CG CD1 CD2 REMARK 470 GLU A 225 CG CD OE1 OE2 REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 ARG A 248 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 255 CG CD1 CD2 REMARK 470 GLN A 256 CG CD OE1 NE2 REMARK 470 TYR A 350 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET A 351 CG SD CE REMARK 470 ARG A 353 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 358 CG CD CE NZ REMARK 470 ARG A 381 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 383 CG CD CE NZ REMARK 470 LYS A 412 CG CD CE NZ REMARK 470 GLU A 414 CG CD OE1 OE2 REMARK 470 ARG A 420 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 423 CG OD1 ND2 REMARK 470 PHE A 442 CG CD1 CD2 CE1 CE2 CZ REMARK 470 CYS A 443 SG REMARK 470 VAL A 454 CG1 CG2 REMARK 470 LEU A 455 CG CD1 CD2 REMARK 470 PRO A 456 CG CD REMARK 470 VAL A 457 CG1 CG2 REMARK 470 ASP A 458 CG OD1 OD2 REMARK 470 VAL A 459 CG1 CG2 REMARK 470 GLN A 460 CG CD OE1 NE2 REMARK 470 THR A 461 OG1 CG2 REMARK 470 LEU A 462 CG CD1 CD2 REMARK 470 ASN A 463 CG OD1 ND2 REMARK 470 SER A 464 OG REMARK 470 VAL A 474 CG1 CG2 REMARK 470 GLN A 475 CG CD OE1 NE2 REMARK 470 ILE A 478 CG1 CG2 CD1 REMARK 470 PHE A 483 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 HIS A 485 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 496 CG OD1 OD2 REMARK 470 PHE A 508 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 464 C SER A 464 O 0.177 REMARK 500 GLY A 466 N GLY A 466 CA 0.100 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 423 N - CA - C ANGL. DEV. = -18.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 64 -66.36 -120.38 REMARK 500 GLU A 69 99.28 -162.97 REMARK 500 ILE A 70 -159.74 -83.95 REMARK 500 LEU A 71 -82.65 -43.11 REMARK 500 LYS A 86 79.76 -112.44 REMARK 500 SER A 123 96.93 -62.55 REMARK 500 GLU A 128 134.04 -38.56 REMARK 500 ASP A 129 -3.79 77.04 REMARK 500 CYS A 151 -56.21 -133.29 REMARK 500 GLN A 152 28.32 -143.00 REMARK 500 PRO A 155 -147.76 -87.08 REMARK 500 LYS A 158 -169.75 -79.49 REMARK 500 ASP A 159 -13.64 57.46 REMARK 500 ALA A 168 -70.24 -97.36 REMARK 500 ARG A 181 22.56 45.85 REMARK 500 ALA A 210 138.64 -170.36 REMARK 500 GLU A 225 107.04 -37.30 REMARK 500 VAL A 231 148.50 -170.38 REMARK 500 ASN A 250 42.71 -104.09 REMARK 500 SER A 251 80.37 49.40 REMARK 500 GLN A 252 -54.12 -128.19 REMARK 500 LEU A 255 107.94 -34.39 REMARK 500 GLN A 256 138.47 -27.85 REMARK 500 ASP A 266 -60.25 -95.50 REMARK 500 SER A 285 131.85 -14.80 REMARK 500 ASP A 327 -73.60 -37.59 REMARK 500 PRO A 341 177.38 -56.89 REMARK 500 MET A 351 72.37 -118.30 REMARK 500 ASN A 352 8.01 59.76 REMARK 500 THR A 356 -0.47 -153.89 REMARK 500 LYS A 358 33.47 -157.61 REMARK 500 ASP A 361 139.19 -173.55 REMARK 500 TYR A 362 147.97 -174.66 REMARK 500 GLU A 366 60.72 -106.42 REMARK 500 GLU A 386 10.85 -61.41 REMARK 500 ASN A 396 -166.78 -125.72 REMARK 500 LEU A 455 156.58 174.67 REMARK 500 VAL A 457 -146.55 -111.02 REMARK 500 VAL A 459 22.20 -150.39 REMARK 500 GLN A 460 -163.13 -167.37 REMARK 500 THR A 461 -169.87 168.62 REMARK 500 ASN A 463 86.32 -154.19 REMARK 500 SER A 480 -5.35 67.19 REMARK 500 ALA A 482 117.07 179.43 REMARK 500 PHE A 483 -157.32 -84.50 REMARK 500 LYS A 484 78.36 91.72 REMARK 500 ASP A 496 -9.38 -53.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 69 ILE A 70 149.10 REMARK 500 ILE A 70 LEU A 71 -145.85 REMARK 500 ASN A 250 SER A 251 144.35 REMARK 500 GLN A 460 THR A 461 -132.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E9W RELATED DB: PDB REMARK 900 SCF-KIT 2:2 COMPLEX REMARK 900 RELATED ID: 1EXZ RELATED DB: PDB REMARK 900 THE FREE FORM OF SCF DBREF 2EC8 A 1 519 UNP P10721 KIT_HUMAN 1 519 SEQADV 2EC8 HIS A 520 UNP P10721 EXPRESSION TAG SEQADV 2EC8 HIS A 521 UNP P10721 EXPRESSION TAG SEQADV 2EC8 HIS A 522 UNP P10721 EXPRESSION TAG SEQADV 2EC8 HIS A 523 UNP P10721 EXPRESSION TAG SEQADV 2EC8 HIS A 524 UNP P10721 EXPRESSION TAG SEQRES 1 A 524 MET ARG GLY ALA ARG GLY ALA TRP ASP PHE LEU CYS VAL SEQRES 2 A 524 LEU LEU LEU LEU LEU ARG VAL GLN THR GLY SER SER GLN SEQRES 3 A 524 PRO SER VAL SER PRO GLY GLU PRO SER PRO PRO SER ILE SEQRES 4 A 524 HIS PRO GLY LYS SER ASP LEU ILE VAL ARG VAL GLY ASP SEQRES 5 A 524 GLU ILE ARG LEU LEU CYS THR ASP PRO GLY PHE VAL LYS SEQRES 6 A 524 TRP THR PHE GLU ILE LEU ASP GLU THR ASN GLU ASN LYS SEQRES 7 A 524 GLN ASN GLU TRP ILE THR GLU LYS ALA GLU ALA THR ASN SEQRES 8 A 524 THR GLY LYS TYR THR CYS THR ASN LYS HIS GLY LEU SER SEQRES 9 A 524 ASN SER ILE TYR VAL PHE VAL ARG ASP PRO ALA LYS LEU SEQRES 10 A 524 PHE LEU VAL ASP ARG SER LEU TYR GLY LYS GLU ASP ASN SEQRES 11 A 524 ASP THR LEU VAL ARG CYS PRO LEU THR ASP PRO GLU VAL SEQRES 12 A 524 THR ASN TYR SER LEU LYS GLY CYS GLN GLY LYS PRO LEU SEQRES 13 A 524 PRO LYS ASP LEU ARG PHE ILE PRO ASP PRO LYS ALA GLY SEQRES 14 A 524 ILE MET ILE LYS SER VAL LYS ARG ALA TYR HIS ARG LEU SEQRES 15 A 524 CYS LEU HIS CYS SER VAL ASP GLN GLU GLY LYS SER VAL SEQRES 16 A 524 LEU SER GLU LYS PHE ILE LEU LYS VAL ARG PRO ALA PHE SEQRES 17 A 524 LYS ALA VAL PRO VAL VAL SER VAL SER LYS ALA SER TYR SEQRES 18 A 524 LEU LEU ARG GLU GLY GLU GLU PHE THR VAL THR CYS THR SEQRES 19 A 524 ILE LYS ASP VAL SER SER SER VAL TYR SER THR TRP LYS SEQRES 20 A 524 ARG GLU ASN SER GLN THR LYS LEU GLN GLU LYS TYR ASN SEQRES 21 A 524 SER TRP HIS HIS GLY ASP PHE ASN TYR GLU ARG GLN ALA SEQRES 22 A 524 THR LEU THR ILE SER SER ALA ARG VAL ASN ASP SER GLY SEQRES 23 A 524 VAL PHE MET CYS TYR ALA ASN ASN THR PHE GLY SER ALA SEQRES 24 A 524 ASN VAL THR THR THR LEU GLU VAL VAL ASP LYS GLY PHE SEQRES 25 A 524 ILE ASN ILE PHE PRO MET ILE ASN THR THR VAL PHE VAL SEQRES 26 A 524 ASN ASP GLY GLU ASN VAL ASP LEU ILE VAL GLU TYR GLU SEQRES 27 A 524 ALA PHE PRO LYS PRO GLU HIS GLN GLN TRP ILE TYR MET SEQRES 28 A 524 ASN ARG THR PHE THR ASP LYS TRP GLU ASP TYR PRO LYS SEQRES 29 A 524 SER GLU ASN GLU SER ASN ILE ARG TYR VAL SER GLU LEU SEQRES 30 A 524 HIS LEU THR ARG LEU LYS GLY THR GLU GLY GLY THR TYR SEQRES 31 A 524 THR PHE LEU VAL SER ASN SER ASP VAL ASN ALA ALA ILE SEQRES 32 A 524 ALA PHE ASN VAL TYR VAL ASN THR LYS PRO GLU ILE LEU SEQRES 33 A 524 THR TYR ASP ARG LEU VAL ASN GLY MET LEU GLN CYS VAL SEQRES 34 A 524 ALA ALA GLY PHE PRO GLU PRO THR ILE ASP TRP TYR PHE SEQRES 35 A 524 CYS PRO GLY THR GLU GLN ARG CYS SER ALA SER VAL LEU SEQRES 36 A 524 PRO VAL ASP VAL GLN THR LEU ASN SER SER GLY PRO PRO SEQRES 37 A 524 PHE GLY LYS LEU VAL VAL GLN SER SER ILE ASP SER SER SEQRES 38 A 524 ALA PHE LYS HIS ASN GLY THR VAL GLU CYS LYS ALA TYR SEQRES 39 A 524 ASN ASP VAL GLY LYS THR SER ALA TYR PHE ASN PHE ALA SEQRES 40 A 524 PHE LYS GLY ASN ASN LYS GLU GLN ILE HIS PRO HIS HIS SEQRES 41 A 524 HIS HIS HIS HIS MODRES 2EC8 ASN A 130 ASN GLYCOSYLATION SITE MODRES 2EC8 ASN A 293 ASN GLYCOSYLATION SITE MODRES 2EC8 ASN A 300 ASN GLYCOSYLATION SITE MODRES 2EC8 ASN A 320 ASN GLYCOSYLATION SITE MODRES 2EC8 ASN A 367 ASN GLYCOSYLATION SITE HET NAG A 700 14 HET NAG A 750 14 HET NAG A 800 14 HET NAG A 850 14 HET NAG A 900 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 5(C8 H15 N O6) HELIX 1 1 LYS A 176 HIS A 180 5 5 HELIX 2 2 LYS A 383 GLY A 387 5 5 SHEET 1 A 3 SER A 38 HIS A 40 0 SHEET 2 A 3 ILE A 54 THR A 59 -1 O LEU A 57 N HIS A 40 SHEET 3 A 3 GLU A 81 THR A 84 -1 O TRP A 82 N LEU A 56 SHEET 1 B 5 ASP A 45 ILE A 47 0 SHEET 2 B 5 SER A 104 PHE A 110 1 O TYR A 108 N LEU A 46 SHEET 3 B 5 GLY A 93 ASN A 99 -1 N GLY A 93 O VAL A 109 SHEET 4 B 5 PHE A 63 GLU A 69 -1 N THR A 67 O THR A 96 SHEET 5 B 5 ASN A 75 ASN A 77 -1 O ASN A 75 N PHE A 68 SHEET 1 C 2 GLY A 126 LYS A 127 0 SHEET 2 C 2 VAL A 204 ARG A 205 1 O ARG A 205 N GLY A 126 SHEET 1 D 3 THR A 132 VAL A 134 0 SHEET 2 D 3 GLY A 169 LYS A 173 -1 O ILE A 170 N VAL A 134 SHEET 3 D 3 ARG A 161 ASP A 165 -1 N ASP A 165 O GLY A 169 SHEET 1 E 3 TYR A 146 LYS A 149 0 SHEET 2 E 3 CYS A 183 VAL A 188 -1 O HIS A 185 N LYS A 149 SHEET 3 E 3 PHE A 200 ILE A 201 -1 O PHE A 200 N LEU A 184 SHEET 1 F 4 VAL A 213 SER A 215 0 SHEET 2 F 4 PHE A 229 ASP A 237 -1 O THR A 234 N SER A 215 SHEET 3 F 4 TYR A 269 ILE A 277 -1 O TYR A 269 N ASP A 237 SHEET 4 F 4 LYS A 258 HIS A 263 -1 N ASN A 260 O GLN A 272 SHEET 1 G 4 SER A 220 ARG A 224 0 SHEET 2 G 4 SER A 298 VAL A 308 1 O VAL A 308 N LEU A 223 SHEET 3 G 4 GLY A 286 ASN A 293 -1 N CYS A 290 O VAL A 301 SHEET 4 G 4 TYR A 243 ARG A 248 -1 N TYR A 243 O ASN A 293 SHEET 1 H 4 PHE A 312 PRO A 317 0 SHEET 2 H 4 VAL A 331 PHE A 340 -1 O PHE A 340 N PHE A 312 SHEET 3 H 4 ARG A 372 LEU A 379 -1 O TYR A 373 N TYR A 337 SHEET 4 H 4 TYR A 362 PRO A 363 -1 N TYR A 362 O VAL A 374 SHEET 1 I 4 THR A 322 VAL A 325 0 SHEET 2 I 4 ASN A 400 VAL A 409 1 O TYR A 408 N VAL A 323 SHEET 3 I 4 GLY A 388 SER A 395 -1 N TYR A 390 O PHE A 405 SHEET 4 I 4 HIS A 345 ILE A 349 -1 N GLN A 347 O LEU A 393 SHEET 1 J 3 THR A 411 ASP A 419 0 SHEET 2 J 3 LEU A 426 PHE A 433 -1 O ALA A 431 N GLU A 414 SHEET 3 J 3 LEU A 472 ILE A 478 -1 O VAL A 474 N ALA A 430 SHEET 1 K 3 THR A 437 ASP A 439 0 SHEET 2 K 3 LYS A 492 TYR A 494 -1 O TYR A 494 N THR A 437 SHEET 3 K 3 LYS A 499 SER A 501 -1 O THR A 500 N ALA A 493 SSBOND 1 CYS A 58 CYS A 97 1555 1555 2.05 SSBOND 2 CYS A 136 CYS A 186 1555 1555 2.05 SSBOND 3 CYS A 151 CYS A 183 1555 1555 2.03 SSBOND 4 CYS A 233 CYS A 290 1555 1555 2.06 SSBOND 5 CYS A 428 CYS A 491 1555 1555 2.04 LINK ND2 ASN A 130 C1 NAG A 700 1555 1555 1.48 LINK ND2 ASN A 293 C1 NAG A 750 1555 1555 1.47 LINK ND2 ASN A 300 C1 NAG A 800 1555 1555 1.56 LINK ND2 ASN A 320 C1 NAG A 900 1555 1555 1.45 LINK ND2 ASN A 367 C1 NAG A 850 1555 1555 1.45 CISPEP 1 HIS A 40 PRO A 41 0 2.14 CISPEP 2 PHE A 340 PRO A 341 0 -3.41 CISPEP 3 PHE A 433 PRO A 434 0 -2.74 CISPEP 4 PRO A 467 PRO A 468 0 3.30 CRYST1 162.249 162.249 67.586 90.00 90.00 120.00 H 3 9 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006163 0.003558 0.000000 0.00000 SCALE2 0.000000 0.007117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014796 0.00000