PDB Short entry for 3S37 HEADER IMMUNE SYSTEM/TRANSFERASE 17-MAY-11 3S37 TITLE STRUCTURAL BASIS FOR THE FUNCTION OF TWO ANTI-VEGF RECEPTOR ANTIBODIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1121B FAB LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 1121B FAB HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 11 CHAIN: X; COMPND 12 FRAGMENT: DOMAIN 3 OF VEGF RECEPTOR 2, UNP RESIDUES 220-338; COMPND 13 SYNONYM: VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN COMPND 14 RECEPTOR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1; COMPND 15 EC: 2.7.10.1; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: MOUSE, HUMAN; SOURCE 4 ORGANISM_TAXID: 10090, 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: MAMMALIAN KIDNEY CELLS HEK293; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: MOUSE, HUMAN; SOURCE 11 ORGANISM_TAXID: 10090, 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: MAMMALIAN KIDNEY CELLS HEK293; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: FLK1, KDR; SOURCE 20 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 22 EXPRESSION_SYSTEM_CELL_LINE: HI5 KEYWDS ANTIBODY, KDR, VEGF RECEPTOR, CANCER, IMMUNE SYSTEM-TRANSFERASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.FRANKLIN REVDAT 2 08-NOV-17 3S37 1 SOURCE REMARK REVDAT 1 24-AUG-11 3S37 0 JRNL AUTH M.C.FRANKLIN,E.C.NAVARRO,Y.WANG,S.PATEL,P.SINGH,Y.ZHANG, JRNL AUTH 2 K.PERSAUD,A.BARI,H.GRIFFITH,L.SHEN,P.BALDERES,P.KUSSIE JRNL TITL THE STRUCTURAL BASIS FOR THE FUNCTION OF TWO ANTI-VEGF JRNL TITL 2 RECEPTOR 2 ANTIBODIES. JRNL REF STRUCTURE V. 19 1097 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21827946 JRNL DOI 10.1016/J.STR.2011.01.019 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15653 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) : 0.284 REMARK 3 R VALUE (WORKING SET) : 0.282 REMARK 3 FREE R VALUE : 0.315 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 831 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1129 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.4270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4037 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.08000 REMARK 3 B12 (A**2) : 0.00000 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): 0.441 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.425 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 46.565 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.898 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4158 ; 0.004 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2788 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5644 ; 0.746 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6825 ; 0.676 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 4.306 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;29.511 ;24.099 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 682 ;10.422 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ; 7.539 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 638 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4619 ; 0.002 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 827 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2654 ; 0.060 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1084 ; 0.007 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4286 ; 0.113 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1504 ; 0.133 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1358 ; 0.227 ; 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 : 5 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 : L 2 L 108 REMARK 3 ORIGIN FOR THE GROUP (A): -32.5045 -2.4449 -7.4541 REMARK 3 T TENSOR REMARK 3 T11: 0.1462 T22: 0.2520 REMARK 3 T33: 0.1813 T12: 0.0604 REMARK 3 T13: -0.0162 T23: -0.0382 REMARK 3 L TENSOR REMARK 3 L11: 3.8882 L22: 4.2777 REMARK 3 L33: 4.4951 L12: -2.7254 REMARK 3 L13: 2.4402 L23: -0.6833 REMARK 3 S TENSOR REMARK 3 S11: -0.1923 S12: -0.2556 S13: 0.3819 REMARK 3 S21: 0.0614 S22: -0.0334 S23: 0.1235 REMARK 3 S31: -0.5537 S32: -0.3359 S33: 0.2258 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 : L 109 L 213 REMARK 3 ORIGIN FOR THE GROUP (A): -10.6884 -19.0067 -26.2317 REMARK 3 T TENSOR REMARK 3 T11: 0.0873 T22: 0.2495 REMARK 3 T33: 0.1392 T12: 0.0075 REMARK 3 T13: -0.0334 T23: 0.0446 REMARK 3 L TENSOR REMARK 3 L11: 1.6490 L22: 2.7464 REMARK 3 L33: 8.6138 L12: 0.2176 REMARK 3 L13: -1.5981 L23: -0.5656 REMARK 3 S TENSOR REMARK 3 S11: -0.0375 S12: 0.2196 S13: -0.1322 REMARK 3 S21: -0.2268 S22: -0.2419 S23: -0.3506 REMARK 3 S31: -0.2999 S32: 0.3984 S33: 0.2794 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 : H 2 H 116 REMARK 3 ORIGIN FOR THE GROUP (A): -45.8405 -5.7932 -25.8639 REMARK 3 T TENSOR REMARK 3 T11: 0.4434 T22: 0.5712 REMARK 3 T33: 0.4988 T12: 0.2807 REMARK 3 T13: -0.3654 T23: -0.1632 REMARK 3 L TENSOR REMARK 3 L11: 5.9480 L22: 6.8987 REMARK 3 L33: 6.7627 L12: -0.9456 REMARK 3 L13: -0.5485 L23: 3.8213 REMARK 3 S TENSOR REMARK 3 S11: 0.0579 S12: 0.3500 S13: 0.1167 REMARK 3 S21: -1.3661 S22: -0.7382 S23: 1.1285 REMARK 3 S31: -0.8158 S32: -1.1445 S33: 0.6802 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 117 H 216 REMARK 3 ORIGIN FOR THE GROUP (A): -21.3643 -31.0593 -27.9856 REMARK 3 T TENSOR REMARK 3 T11: 0.1484 T22: 0.2155 REMARK 3 T33: 0.1578 T12: -0.0081 REMARK 3 T13: -0.0141 T23: -0.1102 REMARK 3 L TENSOR REMARK 3 L11: 3.0870 L22: 5.3933 REMARK 3 L33: 6.9741 L12: 0.1067 REMARK 3 L13: 1.0424 L23: -1.2368 REMARK 3 S TENSOR REMARK 3 S11: -0.0279 S12: 0.0309 S13: -0.3549 REMARK 3 S21: -0.1095 S22: -0.0591 S23: -0.0074 REMARK 3 S31: 0.4597 S32: 0.0345 S33: 0.0870 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 220 X 329 REMARK 3 ORIGIN FOR THE GROUP (A): -65.1669 9.9413 -11.5355 REMARK 3 T TENSOR REMARK 3 T11: 0.7681 T22: 1.0992 REMARK 3 T33: 1.3047 T12: 0.3308 REMARK 3 T13: -0.0459 T23: -0.2085 REMARK 3 L TENSOR REMARK 3 L11: 11.8504 L22: 4.2648 REMARK 3 L33: 8.5435 L12: 1.1183 REMARK 3 L13: -5.4752 L23: -1.2076 REMARK 3 S TENSOR REMARK 3 S11: 0.3604 S12: 0.8899 S13: 0.9488 REMARK 3 S21: 0.1203 S22: -0.0947 S23: 1.4231 REMARK 3 S31: 0.0819 S32: -1.4745 S33: -0.2657 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3S37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 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 : 16605 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE, PH 6.5, 0.1 M CACL2, REMARK 280 40% PEG 1500, 10% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 137.51400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.84200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.84200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 206.27100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.84200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.84200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 68.75700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.84200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.84200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 206.27100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.84200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.84200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.75700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 137.51400 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, X 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 ASP L 1 REMARK 465 CYS L 214 REMARK 465 GLU H 1 REMARK 465 SER H 131 REMARK 465 LYS H 132 REMARK 465 SER H 133 REMARK 465 THR H 134 REMARK 465 SER H 135 REMARK 465 GLY H 136 REMARK 465 LYS H 217 REMARK 465 SER H 218 REMARK 465 CYS H 219 REMARK 465 ALA H 220 REMARK 465 ALA H 221 REMARK 465 ALA X 217 REMARK 465 ASP X 218 REMARK 465 PRO X 219 REMARK 465 VAL X 330 REMARK 465 ALA X 331 REMARK 465 PHE X 332 REMARK 465 GLY X 333 REMARK 465 SER X 334 REMARK 465 GLY X 335 REMARK 465 MET X 336 REMARK 465 GLU X 337 REMARK 465 SER X 338 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 GLU L 213 CG CD OE1 OE2 REMARK 470 GLU X 284 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER H 30 OG SER H 53 1.90 REMARK 500 REMARK 500 REMARK: NULL 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 PRO H 152 CD PRO H 152 N 0.139 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 SER H 25 CB - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 SER H 25 N - CA - C ANGL. DEV. = -23.8 DEGREES REMARK 500 SER H 30 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 ALA H 102 N - CA - CB ANGL. DEV. = 8.8 DEGREES REMARK 500 SER H 115 CB - CA - C ANGL. DEV. = -21.7 DEGREES REMARK 500 SER H 116 N - CA - CB ANGL. DEV. = -24.1 DEGREES REMARK 500 SER H 116 N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 GLU H 151 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 GLU H 151 N - CA - C ANGL. DEV. = 17.1 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 ASP L 30 -120.42 52.88 REMARK 500 ALA L 51 -57.77 75.46 REMARK 500 LYS L 92 -71.22 -121.68 REMARK 500 ASN L 138 74.23 54.41 REMARK 500 SER H 30 -13.06 -43.38 REMARK 500 SER H 31 -51.00 -120.56 REMARK 500 ARG H 67 -56.98 -137.82 REMARK 500 LEU H 81 98.25 -161.30 REMARK 500 THR H 100 80.16 -160.28 REMARK 500 ASP H 101 -63.86 90.19 REMARK 500 SER X 283 -114.75 50.66 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 SER H 30 SER H 31 -146.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3S34 RELATED DB: PDB REMARK 900 RELATED ID: 3S36 RELATED DB: PDB DBREF 3S37 X 220 338 UNP P35968 VGFR2_HUMAN 220 338 DBREF 3S37 L 1 214 PDB 3S37 3S37 1 214 DBREF 3S37 H 1 221 PDB 3S37 3S37 1 221 SEQADV 3S37 ALA X 217 UNP P35968 EXPRESSION TAG SEQADV 3S37 ASP X 218 UNP P35968 EXPRESSION TAG SEQADV 3S37 PRO X 219 UNP P35968 EXPRESSION TAG SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO SER SER VAL SER ALA SEQRES 2 L 214 SER ILE GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN GLY ILE ASP ASN TRP LEU GLY TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 L 214 ASN LEU ASP THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR TYR PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN ALA GLU ASP PHE ALA VAL TYR PHE CYS GLN GLN ALA SEQRES 8 L 214 LYS ALA PHE PRO PRO THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 214 ASP ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS SEQRES 1 H 221 GLU VAL GLN LEU VAL GLN SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 221 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 221 PHE THR PHE SER SER TYR SER MET ASN TRP VAL ARG GLN SEQRES 4 H 221 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER SER ILE SER SEQRES 5 H 221 SER SER SER SER TYR ILE TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 221 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 221 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 221 ALA VAL TYR TYR CYS ALA ARG VAL THR ASP ALA PHE ASP SEQRES 9 H 221 ILE TRP GLY GLN GLY THR MET VAL THR VAL SER SER ALA SEQRES 10 H 221 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SEQRES 11 H 221 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS SEQRES 12 H 221 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 221 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 221 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 221 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN SEQRES 16 H 221 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR SEQRES 17 H 221 LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS ALA ALA SEQRES 1 X 122 ALA ASP PRO GLY TYR ARG ILE TYR ASP VAL VAL LEU SER SEQRES 2 X 122 PRO SER HIS GLY ILE GLU LEU SER VAL GLY GLU LYS LEU SEQRES 3 X 122 VAL LEU ASN CYS THR ALA ARG THR GLU LEU ASN VAL GLY SEQRES 4 X 122 ILE ASP PHE ASN TRP GLU TYR PRO SER SER LYS HIS GLN SEQRES 5 X 122 HIS LYS LYS LEU VAL ASN ARG ASP LEU LYS THR GLN SER SEQRES 6 X 122 GLY SER GLU MET LYS LYS PHE LEU SER THR LEU THR ILE SEQRES 7 X 122 ASP GLY VAL THR ARG SER ASP GLN GLY LEU TYR THR CYS SEQRES 8 X 122 ALA ALA SER SER GLY LEU MET THR LYS LYS ASN SER THR SEQRES 9 X 122 PHE VAL ARG VAL HIS GLU LYS PRO PHE VAL ALA PHE GLY SEQRES 10 X 122 SER GLY MET GLU SER HELIX 1 1 GLN L 79 PHE L 83 5 5 HELIX 2 2 SER L 121 LYS L 126 1 6 HELIX 3 3 LYS L 183 HIS L 189 1 7 HELIX 4 4 ARG H 87 THR H 91 5 5 HELIX 5 5 SER H 159 ALA H 161 5 3 HELIX 6 6 SER H 190 LEU H 192 5 3 HELIX 7 7 PRO H 205 ASN H 207 5 3 HELIX 8 8 THR X 298 GLN X 302 5 5 SHEET 1 A 4 MET L 4 SER L 7 0 SHEET 2 A 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 A 4 TYR L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 B 6 SER L 10 ALA L 13 0 SHEET 2 B 6 THR L 102 ILE L 106 1 O LYS L 103 N VAL L 11 SHEET 3 B 6 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N TYR L 36 O PHE L 87 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 SER L 114 PHE L 118 0 SHEET 2 C 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 C 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 C 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 D 4 ALA L 153 GLN L 155 0 SHEET 2 D 4 LYS L 145 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 D 4 VAL L 191 THR L 197 -1 O ALA L 193 N LYS L 149 SHEET 4 D 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 E 4 GLN H 3 SER H 7 0 SHEET 2 E 4 SER H 21 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 E 4 SER H 78 MET H 83 -1 O LEU H 79 N CYS H 22 SHEET 4 E 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 F 6 LEU H 11 VAL H 12 0 SHEET 2 F 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 F 6 ALA H 92 VAL H 99 -1 N TYR H 94 O THR H 110 SHEET 4 F 6 SER H 33 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 F 6 LEU H 45 ILE H 51 -1 O SER H 49 N TRP H 36 SHEET 6 F 6 ILE H 58 TYR H 60 -1 O TYR H 59 N SER H 50 SHEET 1 G 4 LEU H 11 VAL H 12 0 SHEET 2 G 4 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 G 4 ALA H 92 VAL H 99 -1 N TYR H 94 O THR H 110 SHEET 4 G 4 ILE H 105 TRP H 106 -1 O ILE H 105 N ARG H 98 SHEET 1 H 4 SER H 123 LEU H 127 0 SHEET 2 H 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 H 4 TYR H 179 PRO H 188 -1 O LEU H 181 N VAL H 145 SHEET 4 H 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 I 4 SER H 123 LEU H 127 0 SHEET 2 I 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 I 4 TYR H 179 PRO H 188 -1 O LEU H 181 N VAL H 145 SHEET 4 I 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 J 3 VAL H 153 TRP H 157 0 SHEET 2 J 3 TYR H 197 HIS H 203 -1 O ASN H 200 N SER H 156 SHEET 3 J 3 THR H 208 VAL H 214 -1 O VAL H 210 N VAL H 201 SHEET 1 K 4 ILE X 223 SER X 229 0 SHEET 2 K 4 LEU X 242 THR X 250 -1 O ARG X 249 N TYR X 224 SHEET 3 K 4 MET X 285 ILE X 294 -1 O LYS X 286 N THR X 250 SHEET 4 K 4 LYS X 278 GLY X 282 -1 N GLN X 280 O LYS X 287 SHEET 1 L 4 ILE X 234 SER X 237 0 SHEET 2 L 4 THR X 315 HIS X 325 1 O ARG X 323 N LEU X 236 SHEET 3 L 4 GLY X 303 SER X 310 -1 N TYR X 305 O THR X 320 SHEET 4 L 4 ASP X 257 GLU X 261 -1 N ASN X 259 O ALA X 308 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 4 CYS H 143 CYS H 199 1555 1555 2.03 SSBOND 5 CYS X 246 CYS X 307 1555 1555 2.03 CISPEP 1 SER L 7 PRO L 8 0 -5.72 CISPEP 2 TYR L 140 PRO L 141 0 6.47 CISPEP 3 PHE H 149 PRO H 150 0 -3.32 CISPEP 4 SER X 229 PRO X 230 0 -2.07 CRYST1 63.684 63.684 275.028 90.00 90.00 90.00 P 43 21 2 8 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 0.015703 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003636 0.00000