PDB Short entry for 2C9Y HEADER TRANSFERASE 15-DEC-05 2C9Y TITLE STRUCTURE OF HUMAN ADENYLATE KINASE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-AMP TRANSPHOSPHORYLASE; COMPND 5 EC: 2.7.4.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLIC-SGC KEYWDS NUCLEOTIDE KINASE, TRANSFERASE, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.BUNKOCZI,P.FILIPPAKOPOULOS,J.E.DEBRECZENI,A.TURNBULL, AUTHOR 2 E.PAPAGRIGORIOU,P.SAVITSKY,S.COLEBROOK,F.VON DELFT,C.ARROWSMITH, AUTHOR 3 A.EDWARDS,M.SUNDSTROM,J.WEIGELT,S.KNAPP REVDAT 6 13-DEC-23 2C9Y 1 REMARK REVDAT 5 28-FEB-18 2C9Y 1 SOURCE REVDAT 4 24-JAN-18 2C9Y 1 AUTHOR JRNL REVDAT 3 13-JUL-11 2C9Y 1 VERSN REVDAT 2 24-FEB-09 2C9Y 1 VERSN REVDAT 1 04-JAN-06 2C9Y 0 JRNL AUTH G.BUNKOCZI,P.FILIPPAKOPOULOS,J.E.DEBRECZENI,A.TURNBULL, JRNL AUTH 2 E.PAPAGRIGORIOU,P.SAVITSKY,S.COLEBROOK,F.VON DELFT, JRNL AUTH 3 C.ARROWSMITH,A.EDWARDS,M.SUNDSTROM,J.WEIGELT,S.KNAPP JRNL TITL STRUCTURE OF HUMAN ADENYLATE KINASE 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16279 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 895 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1194 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1666 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 151 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) : 26.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : 0.22000 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): 0.198 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.888 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1821 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1276 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2470 ; 1.768 ; 2.056 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3118 ; 0.998 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 217 ; 6.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;34.981 ;23.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 328 ;16.996 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.296 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1909 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 339 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 395 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1279 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 848 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 971 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 126 ; 0.212 ; 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): 8 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 74 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.262 ; 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): 1128 ; 2.444 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1765 ; 3.656 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 789 ; 5.970 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 705 ; 8.215 ;11.000 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 41 REMARK 3 RESIDUE RANGE : A 94 A 130 REMARK 3 RESIDUE RANGE : A 193 A 232 REMARK 3 ORIGIN FOR THE GROUP (A): 1.8112 1.4327 -20.0821 REMARK 3 T TENSOR REMARK 3 T11: -0.1109 T22: -0.1303 REMARK 3 T33: -0.0814 T12: -0.0205 REMARK 3 T13: 0.0688 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 1.3116 L22: 1.2598 REMARK 3 L33: 2.3033 L12: -0.0516 REMARK 3 L13: 0.2810 L23: 0.1630 REMARK 3 S TENSOR REMARK 3 S11: 0.1182 S12: -0.2347 S13: 0.1076 REMARK 3 S21: -0.0672 S22: -0.0512 S23: -0.1459 REMARK 3 S31: 0.1757 S32: 0.0780 S33: -0.0670 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 42 A 93 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6883 13.4305 -24.2732 REMARK 3 T TENSOR REMARK 3 T11: -0.0824 T22: -0.0694 REMARK 3 T33: -0.0431 T12: 0.0402 REMARK 3 T13: 0.0823 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 3.3917 L22: 1.1629 REMARK 3 L33: 2.3004 L12: -0.3455 REMARK 3 L13: -0.4904 L23: 0.6587 REMARK 3 S TENSOR REMARK 3 S11: 0.0957 S12: -0.0487 S13: 0.2655 REMARK 3 S21: -0.0674 S22: -0.0567 S23: 0.1324 REMARK 3 S31: -0.2722 S32: -0.4708 S33: -0.0390 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 131 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1294 6.6709 3.6530 REMARK 3 T TENSOR REMARK 3 T11: -0.0277 T22: 0.1950 REMARK 3 T33: -0.0526 T12: -0.0201 REMARK 3 T13: 0.0259 T23: -0.0573 REMARK 3 L TENSOR REMARK 3 L11: 1.2633 L22: 3.0007 REMARK 3 L33: 2.7115 L12: 0.1537 REMARK 3 L13: 0.1508 L23: 1.0672 REMARK 3 S TENSOR REMARK 3 S11: -0.0249 S12: -0.4814 S13: 0.2399 REMARK 3 S21: 0.4494 S22: 0.0693 S23: -0.1387 REMARK 3 S31: 0.0772 S32: -0.1359 S33: -0.0443 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 : A 1233 A 1233 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2811 9.1070 -3.3066 REMARK 3 T TENSOR REMARK 3 T11: 0.0031 T22: 0.1548 REMARK 3 T33: -0.0173 T12: -0.0105 REMARK 3 T13: 0.0443 T23: -0.1409 REMARK 3 L TENSOR REMARK 3 L11: 0.7280 L22: 7.4232 REMARK 3 L33: 1.9810 L12: 2.3246 REMARK 3 L13: -1.2009 L23: -3.8348 REMARK 3 S TENSOR REMARK 3 S11: 0.1180 S12: 0.0101 S13: 0.0495 REMARK 3 S21: 0.5159 S22: -0.2853 S23: 0.6345 REMARK 3 S31: -0.0436 S32: -0.0041 S33: 0.1673 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 2C9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979097 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17233 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.120 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.98 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: PDB ENTRY 1AK2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH=5.7, 28% PEG3350, PH REMARK 280 5.70 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.52100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.50050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.50050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.52100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.63000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 SER A 4 REMARK 465 VAL A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 TYR A 12 REMARK 465 PRO A 13 REMARK 465 LYS A 14 REMARK 465 LYS A 233 REMARK 465 ASP A 234 REMARK 465 LEU A 235 REMARK 465 VAL A 236 REMARK 465 MET A 237 REMARK 465 PHE A 238 REMARK 465 ILE A 239 REMARK 465 LEU A 240 REMARK 465 GLN A 241 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 LYS A 63 CE NZ REMARK 470 LYS A 72 CE NZ REMARK 470 ARG A 103 NE CZ NH1 NH2 REMARK 470 ARG A 142 NE CZ NH1 NH2 REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LEU A 183 CG CD1 CD2 REMARK 470 GLN A 193 CD OE1 NE2 REMARK 470 LYS A 229 CD CE NZ 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 HOH A 2021 O HOH A 2022 2.00 REMARK 500 O HOH A 2068 O HOH A 2072 2.19 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 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ILE A 16 149.35 -172.94 REMARK 500 THR A 140 -77.63 -84.60 REMARK 500 ARG A 142 174.27 -59.52 REMARK 500 ASN A 157 55.91 -161.43 REMARK 500 THR A 168 -157.85 -89.09 REMARK 500 ASP A 177 144.66 79.69 REMARK 500 ASN A 179 104.65 -47.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B4P A1233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1235 DBREF 2C9Y A 1 239 UNP P54819 KAD2_HUMAN 1 239 SEQADV 2C9Y SER A 0 UNP P54819 EXPRESSION TAG SEQADV 2C9Y LEU A 240 UNP P54819 EXPRESSION TAG SEQADV 2C9Y GLN A 241 UNP P54819 EXPRESSION TAG SEQRES 1 A 242 SER MET ALA PRO SER VAL PRO ALA ALA GLU PRO GLU TYR SEQRES 2 A 242 PRO LYS GLY ILE ARG ALA VAL LEU LEU GLY PRO PRO GLY SEQRES 3 A 242 ALA GLY LYS GLY THR GLN ALA PRO ARG LEU ALA GLU ASN SEQRES 4 A 242 PHE CYS VAL CYS HIS LEU ALA THR GLY ASP MET LEU ARG SEQRES 5 A 242 ALA MET VAL ALA SER GLY SER GLU LEU GLY LYS LYS LEU SEQRES 6 A 242 LYS ALA THR MET ASP ALA GLY LYS LEU VAL SER ASP GLU SEQRES 7 A 242 MET VAL VAL GLU LEU ILE GLU LYS ASN LEU GLU THR PRO SEQRES 8 A 242 LEU CYS LYS ASN GLY PHE LEU LEU ASP GLY PHE PRO ARG SEQRES 9 A 242 THR VAL ARG GLN ALA GLU MET LEU ASP ASP LEU MET GLU SEQRES 10 A 242 LYS ARG LYS GLU LYS LEU ASP SER VAL ILE GLU PHE SER SEQRES 11 A 242 ILE PRO ASP SER LEU LEU ILE ARG ARG ILE THR GLY ARG SEQRES 12 A 242 LEU ILE HIS PRO LYS SER GLY ARG SER TYR HIS GLU GLU SEQRES 13 A 242 PHE ASN PRO PRO LYS GLU PRO MET LYS ASP ASP ILE THR SEQRES 14 A 242 GLY GLU PRO LEU ILE ARG ARG SER ASP ASP ASN GLU LYS SEQRES 15 A 242 ALA LEU LYS ILE ARG LEU GLN ALA TYR HIS THR GLN THR SEQRES 16 A 242 THR PRO LEU ILE GLU TYR TYR ARG LYS ARG GLY ILE HIS SEQRES 17 A 242 SER ALA ILE ASP ALA SER GLN THR PRO ASP VAL VAL PHE SEQRES 18 A 242 ALA SER ILE LEU ALA ALA PHE SER LYS ALA THR CYS LYS SEQRES 19 A 242 ASP LEU VAL MET PHE ILE LEU GLN HET B4P A1233 80 HET EDO A1234 8 HET EDO A1235 4 HETNAM B4P BIS(ADENOSINE)-5'-TETRAPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 B4P C20 H28 N10 O19 P4 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *151(H2 O) HELIX 1 1 GLY A 27 CYS A 40 1 14 HELIX 2 2 THR A 46 GLY A 57 1 12 HELIX 3 3 SER A 58 ALA A 70 1 13 HELIX 4 4 SER A 75 GLU A 88 1 14 HELIX 5 5 THR A 89 LYS A 93 5 5 HELIX 6 6 THR A 104 ARG A 118 1 15 HELIX 7 7 PRO A 131 GLY A 141 1 11 HELIX 8 8 ASN A 179 ARG A 204 1 26 HELIX 9 9 THR A 215 THR A 231 1 17 SHEET 1 AA 5 CYS A 42 ALA A 45 0 SHEET 2 AA 5 GLY A 95 ASP A 99 1 O GLY A 95 N CYS A 42 SHEET 3 AA 5 ILE A 16 LEU A 21 1 O ILE A 16 N PHE A 96 SHEET 4 AA 5 SER A 124 SER A 129 1 O SER A 124 N VAL A 19 SHEET 5 AA 5 HIS A 207 ASP A 211 1 O SER A 208 N GLU A 127 SHEET 1 AB 3 SER A 151 TYR A 152 0 SHEET 2 AB 3 LEU A 143 ILE A 144 -1 O LEU A 143 N TYR A 152 SHEET 3 AB 3 ILE A 173 ARG A 174 -1 O ILE A 173 N ILE A 144 SSBOND 1 CYS A 42 CYS A 92 1555 1555 2.06 CISPEP 1 PHE A 101 PRO A 102 0 -8.04 SITE 1 AC1 20 PRO A 24 GLY A 25 ALA A 26 GLY A 27 SITE 2 AC1 20 GLY A 29 THR A 30 ARG A 138 ARG A 150 SITE 3 AC1 20 SER A 151 PHE A 156 LYS A 160 ARG A 175 SITE 4 AC1 20 GLN A 214 THR A 215 PRO A 216 HOH A2006 SITE 5 AC1 20 HOH A2146 HOH A2148 HOH A2149 HOH A2150 SITE 1 AC2 8 LEU A 87 GLU A 88 THR A 89 LYS A 93 SITE 2 AC2 8 ARG A 118 LYS A 203 ARG A 204 HOH A2079 SITE 1 AC3 7 ASN A 38 ASP A 69 GLY A 71 ARG A 174 SITE 2 AC3 7 PHE A 220 HOH A2013 HOH A2151 CRYST1 45.042 49.260 127.001 90.00 90.00 90.00 P 21 21 21 4 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 0.022202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007874 0.00000