HEADER APOPTOSIS 14-AUG-17 5OQW TITLE XIAP IN COMPLEX WITH SMALL MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE XIAP; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4,IAP-LIKE COMPND 5 PROTEIN,HILP,INHIBITOR OF APOPTOSIS PROTEIN 3,HIAP3,RING-TYPE E3 COMPND 6 UBIQUITIN TRANSFERASE XIAP,X-LINKED INHIBITOR OF APOPTOSIS PROTEIN,X- COMPND 7 LINKED IAP; COMPND 8 EC: 2.3.2.27; COMPND 9 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: XIAP, API3, BIRC4, IAP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28B KEYWDS XIAP, PROTEASE INHIBITOR, APOPTOSIS REGULATION, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR P.A.WILLIAMS REVDAT 4 08-MAY-24 5OQW 1 LINK REVDAT 3 16-OCT-19 5OQW 1 REMARK REVDAT 2 11-JUL-18 5OQW 1 JRNL REVDAT 1 27-JUN-18 5OQW 0 JRNL AUTH G.A.WARD,E.J.LEWIS,J.S.AHN,C.N.JOHNSON,J.F.LYONS,V.MARTINS, JRNL AUTH 2 J.M.MUNCK,S.J.RICH,T.SMYTH,N.T.THOMPSON,P.A.WILLIAMS, JRNL AUTH 3 N.E.WILSHER,N.G.WALLIS,G.CHESSARI JRNL TITL ASTX660, A NOVEL NON-PEPTIDOMIMETIC ANTAGONIST OF CIAP1/2 JRNL TITL 2 AND XIAP, POTENTLY INDUCES TNF ALPHA-DEPENDENT APOPTOSIS IN JRNL TITL 3 CANCER CELL LINES AND INHIBITS TUMOR GROWTH. JRNL REF MOL. CANCER THER. V. 17 1381 2018 JRNL REFN ESSN 1538-8514 JRNL PMID 29695633 JRNL DOI 10.1158/1535-7163.MCT-17-0848 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22829 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1188 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) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1740 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.15000 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): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1889 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1634 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2573 ; 1.325 ; 1.913 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3817 ; 0.969 ; 2.892 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 213 ; 6.445 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;35.050 ;24.061 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 321 ;15.421 ;15.280 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;11.402 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 244 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2086 ; 0.001 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 404 ; 0.000 ; 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): 852 ; 2.510 ; 6.050 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 851 ; 2.492 ; 6.037 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1037 ; 2.973 ; 7.302 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1038 ; 2.972 ; 7.308 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2247 ; 7.826 ;33.822 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2230 ; 7.791 ;33.366 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 : 2 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 249 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 31.5738 -6.9675 -22.6415 REMARK 3 T TENSOR REMARK 3 T11: 0.2948 T22: 0.3521 REMARK 3 T33: 0.0054 T12: -0.0196 REMARK 3 T13: -0.0019 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 4.3262 L22: 4.8593 REMARK 3 L33: 3.7019 L12: 2.0455 REMARK 3 L13: 0.6954 L23: 0.5649 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: 0.3532 S13: 0.0554 REMARK 3 S21: -0.3572 S22: 0.1288 S23: 0.0067 REMARK 3 S31: -0.0502 S32: -0.1981 S33: -0.1049 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 : B 248 B 401 REMARK 3 ORIGIN FOR THE GROUP (A): 32.5499 9.1550 -4.5101 REMARK 3 T TENSOR REMARK 3 T11: 0.2928 T22: 0.3749 REMARK 3 T33: 0.0085 T12: 0.0856 REMARK 3 T13: 0.0067 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 3.6090 L22: 6.7978 REMARK 3 L33: 3.5954 L12: -1.4655 REMARK 3 L13: -0.1888 L23: -0.3718 REMARK 3 S TENSOR REMARK 3 S11: 0.0575 S12: -0.1787 S13: 0.0332 REMARK 3 S21: 0.1630 S22: -0.0279 S23: 0.0096 REMARK 3 S31: -0.0368 S32: -0.3078 S33: -0.0296 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5OQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24134 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 72.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.15800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES/NAOHPH=8, 2.9M NACL, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 53.36650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.69000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.68325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.69000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.69000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.04975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.69000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.69000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.68325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.69000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 80.04975 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 53.36650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 228 REMARK 465 GLY A 229 REMARK 465 SER A 230 REMARK 465 SER A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 SER A 238 REMARK 465 SER A 239 REMARK 465 GLY A 240 REMARK 465 LEU A 241 REMARK 465 VAL A 242 REMARK 465 PRO A 243 REMARK 465 ARG A 244 REMARK 465 GLY A 245 REMARK 465 SER A 246 REMARK 465 HIS A 247 REMARK 465 MET A 248 REMARK 465 MET B 228 REMARK 465 GLY B 229 REMARK 465 SER B 230 REMARK 465 SER B 231 REMARK 465 HIS B 232 REMARK 465 HIS B 233 REMARK 465 HIS B 234 REMARK 465 HIS B 235 REMARK 465 HIS B 236 REMARK 465 HIS B 237 REMARK 465 SER B 238 REMARK 465 SER B 239 REMARK 465 GLY B 240 REMARK 465 LEU B 241 REMARK 465 VAL B 242 REMARK 465 PRO B 243 REMARK 465 ARG B 244 REMARK 465 GLY B 245 REMARK 465 SER B 246 REMARK 465 HIS B 247 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 HIS A 302 -60.83 -95.02 REMARK 500 TRP B 275 108.96 -160.92 REMARK 500 HIS B 302 -61.14 -92.23 REMARK 500 GLN B 336 -38.10 -38.72 REMARK 500 LEU B 352 -78.87 -140.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 610 DISTANCE = 6.11 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 272 O REMARK 620 2 PHE A 272 O 0.0 REMARK 620 3 HOH A 579 O 74.5 74.5 REMARK 620 4 HOH A 579 O 133.9 133.9 84.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 SG REMARK 620 2 CYS A 303 SG 108.0 REMARK 620 3 HIS A 320 NE2 96.7 118.2 REMARK 620 4 CYS A 327 SG 109.9 118.3 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 300 SG REMARK 620 2 CYS B 303 SG 106.7 REMARK 620 3 HIS B 320 NE2 95.8 116.9 REMARK 620 4 CYS B 327 SG 118.6 113.3 104.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A4E A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A4E B 402 DBREF 5OQW A 249 354 UNP P98170 XIAP_HUMAN 249 354 DBREF 5OQW B 249 354 UNP P98170 XIAP_HUMAN 249 354 SEQADV 5OQW MET A 228 UNP P98170 INITIATING METHIONINE SEQADV 5OQW GLY A 229 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER A 230 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER A 231 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 232 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 233 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 234 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 235 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 236 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 237 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER A 238 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER A 239 UNP P98170 EXPRESSION TAG SEQADV 5OQW GLY A 240 UNP P98170 EXPRESSION TAG SEQADV 5OQW LEU A 241 UNP P98170 EXPRESSION TAG SEQADV 5OQW VAL A 242 UNP P98170 EXPRESSION TAG SEQADV 5OQW PRO A 243 UNP P98170 EXPRESSION TAG SEQADV 5OQW ARG A 244 UNP P98170 EXPRESSION TAG SEQADV 5OQW GLY A 245 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER A 246 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS A 247 UNP P98170 EXPRESSION TAG SEQADV 5OQW MET A 248 UNP P98170 EXPRESSION TAG SEQADV 5OQW MET B 228 UNP P98170 INITIATING METHIONINE SEQADV 5OQW GLY B 229 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER B 230 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER B 231 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 232 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 233 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 234 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 235 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 236 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 237 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER B 238 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER B 239 UNP P98170 EXPRESSION TAG SEQADV 5OQW GLY B 240 UNP P98170 EXPRESSION TAG SEQADV 5OQW LEU B 241 UNP P98170 EXPRESSION TAG SEQADV 5OQW VAL B 242 UNP P98170 EXPRESSION TAG SEQADV 5OQW PRO B 243 UNP P98170 EXPRESSION TAG SEQADV 5OQW ARG B 244 UNP P98170 EXPRESSION TAG SEQADV 5OQW GLY B 245 UNP P98170 EXPRESSION TAG SEQADV 5OQW SER B 246 UNP P98170 EXPRESSION TAG SEQADV 5OQW HIS B 247 UNP P98170 EXPRESSION TAG SEQADV 5OQW MET B 248 UNP P98170 EXPRESSION TAG SEQRES 1 A 127 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 127 LEU VAL PRO ARG GLY SER HIS MET ASN PHE PRO ASN SER SEQRES 3 A 127 THR ASN LEU PRO ARG ASN PRO SER MET ALA ASP TYR GLU SEQRES 4 A 127 ALA ARG ILE PHE THR PHE GLY THR TRP ILE TYR SER VAL SEQRES 5 A 127 ASN LYS GLU GLN LEU ALA ARG ALA GLY PHE TYR ALA LEU SEQRES 6 A 127 GLY GLU GLY ASP LYS VAL LYS CYS PHE HIS CYS GLY GLY SEQRES 7 A 127 GLY LEU THR ASP TRP LYS PRO SER GLU ASP PRO TRP GLU SEQRES 8 A 127 GLN HIS ALA LYS TRP TYR PRO GLY CYS LYS TYR LEU LEU SEQRES 9 A 127 GLU GLN LYS GLY GLN GLU TYR ILE ASN ASN ILE HIS LEU SEQRES 10 A 127 THR HIS SER LEU GLU GLU CYS LEU VAL ARG SEQRES 1 B 127 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 127 LEU VAL PRO ARG GLY SER HIS MET ASN PHE PRO ASN SER SEQRES 3 B 127 THR ASN LEU PRO ARG ASN PRO SER MET ALA ASP TYR GLU SEQRES 4 B 127 ALA ARG ILE PHE THR PHE GLY THR TRP ILE TYR SER VAL SEQRES 5 B 127 ASN LYS GLU GLN LEU ALA ARG ALA GLY PHE TYR ALA LEU SEQRES 6 B 127 GLY GLU GLY ASP LYS VAL LYS CYS PHE HIS CYS GLY GLY SEQRES 7 B 127 GLY LEU THR ASP TRP LYS PRO SER GLU ASP PRO TRP GLU SEQRES 8 B 127 GLN HIS ALA LYS TRP TYR PRO GLY CYS LYS TYR LEU LEU SEQRES 9 B 127 GLU GLN LYS GLY GLN GLU TYR ILE ASN ASN ILE HIS LEU SEQRES 10 B 127 THR HIS SER LEU GLU GLU CYS LEU VAL ARG HET ZN A 401 1 HET NA A 402 1 HET A4E A 403 82 HET ZN B 401 1 HET A4E B 402 82 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM A4E 1-[6-[(4-FLUOROPHENYL)METHYL]-5-(HYDROXYMETHYL)-3,3- HETNAM 2 A4E DIMETHYL-2~{H}-PYRROLO[3,2-B]PYRIDIN-1-YL]-2-[(2~{R}, HETNAM 3 A4E 5~{R})-5-METHYL-2-[[(3~{R})-3-METHYLMORPHOLIN-4- HETNAM 4 A4E YL]METHYL]PIPERAZIN-4-IUM-1-YL]ETHANONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NA NA 1+ FORMUL 5 A4E 2(C30 H43 F N5 O3 1+) FORMUL 8 HOH *224(H2 O) HELIX 1 AA1 ASN A 259 ALA A 263 5 5 HELIX 2 AA2 ASP A 264 THR A 271 1 8 HELIX 3 AA3 ASN A 280 ALA A 287 1 8 HELIX 4 AA4 ASP A 315 TYR A 324 1 10 HELIX 5 AA5 CYS A 327 GLY A 335 1 9 HELIX 6 AA6 GLY A 335 ARG A 354 1 20 HELIX 7 AA7 ASN B 259 ALA B 263 5 5 HELIX 8 AA8 ASP B 264 GLY B 273 1 10 HELIX 9 AA9 ASN B 280 ALA B 287 1 8 HELIX 10 AB1 ASP B 315 TYR B 324 1 10 HELIX 11 AB2 CYS B 327 GLY B 335 1 9 HELIX 12 AB3 GLY B 335 CYS B 351 1 17 SHEET 1 AA1 3 PHE A 289 ALA A 291 0 SHEET 2 AA1 3 VAL A 298 CYS A 300 -1 O LYS A 299 N TYR A 290 SHEET 3 AA1 3 GLY A 306 LEU A 307 -1 O LEU A 307 N VAL A 298 SHEET 1 AA2 3 PHE B 289 ALA B 291 0 SHEET 2 AA2 3 VAL B 298 CYS B 300 -1 O LYS B 299 N TYR B 290 SHEET 3 AA2 3 GLY B 306 LEU B 307 -1 O LEU B 307 N VAL B 298 LINK O PHE A 272 NA NA A 402 1555 1555 2.78 LINK O PHE A 272 NA NA A 402 1555 8554 2.73 LINK SG CYS A 300 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 303 ZN ZN A 401 1555 1555 2.27 LINK NE2 HIS A 320 ZN ZN A 401 1555 1555 2.18 LINK SG CYS A 327 ZN ZN A 401 1555 1555 2.23 LINK NA NA A 402 O HOH A 579 1555 1555 2.58 LINK NA NA A 402 O HOH A 579 1555 8554 2.50 LINK SG CYS B 300 ZN ZN B 401 1555 1555 2.25 LINK SG CYS B 303 ZN ZN B 401 1555 1555 2.23 LINK NE2 HIS B 320 ZN ZN B 401 1555 1555 2.17 LINK SG CYS B 327 ZN ZN B 401 1555 1555 2.26 SITE 1 AC1 4 CYS A 300 CYS A 303 HIS A 320 CYS A 327 SITE 1 AC2 4 THR A 271 PHE A 272 THR A 274 HOH A 579 SITE 1 AC3 15 LEU A 292 VAL A 298 LYS A 299 GLY A 306 SITE 2 AC3 15 LEU A 307 THR A 308 ASP A 309 TRP A 310 SITE 3 AC3 15 GLU A 314 GLN A 319 TRP A 323 TYR A 324 SITE 4 AC3 15 HOH A 556 HOH A 561 HOH A 565 SITE 1 AC4 4 CYS B 300 CYS B 303 HIS B 320 CYS B 327 SITE 1 AC5 14 VAL B 298 LYS B 299 GLY B 306 LEU B 307 SITE 2 AC5 14 THR B 308 ASP B 309 TRP B 310 GLU B 314 SITE 3 AC5 14 GLN B 319 TRP B 323 TYR B 324 HOH B 544 SITE 4 AC5 14 HOH B 546 HOH B 556 CRYST1 99.380 99.380 106.733 90.00 90.00 90.00 P 41 21 2 16 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 0.010062 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009369 0.00000