PDB Short entry for 5C3K HEADER APOPTOSIS 17-JUN-15 5C3K TITLE FRAGMENT-BASED DRUG DISCOVERY TARGETING INHIBITOR OF APOPTOSIS TITLE 2 PROTEINS: COMPOUND 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE XIAP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 249-354; COMPND 5 SYNONYM: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4,IAP-LIKE COMPND 6 PROTEIN,HILP,INHIBITOR OF APOPTOSIS PROTEIN 3,HIAP3,X-LINKED COMPND 7 INHIBITOR OF APOPTOSIS PROTEIN,X-LINKED IAP; COMPND 8 EC: 6.3.2.-; 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_PLASMID: PET 28B KEYWDS LIGASE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR G.CHESSARI,I.M.BUCK,J.E.H.DAY,P.J.DAY,A.IQBAL,C.N.JOHNSON,E.J.LEWIS, AUTHOR 2 V.MARTINS,D.MILLER,M.READER,D.C.REES,S.J.RICH,E.TAMANINI,M.VITORINO, AUTHOR 3 G.A.WARD,P.A.WILLIAMS,G.WILLIAMS,N.E.WILSHER,A.J.-A.WOOLFORD REVDAT 4 10-JAN-24 5C3K 1 REMARK REVDAT 3 29-NOV-17 5C3K 1 REMARK REVDAT 2 09-SEP-15 5C3K 1 JRNL REVDAT 1 12-AUG-15 5C3K 0 JRNL AUTH G.CHESSARI,I.M.BUCK,J.E.DAY,P.J.DAY,A.IQBAL,C.N.JOHNSON, JRNL AUTH 2 E.J.LEWIS,V.MARTINS,D.MILLER,M.READER,D.C.REES,S.J.RICH, JRNL AUTH 3 E.TAMANINI,M.VITORINO,G.A.WARD,P.A.WILLIAMS,G.WILLIAMS, JRNL AUTH 4 N.E.WILSHER,A.J.WOOLFORD JRNL TITL FRAGMENT-BASED DRUG DISCOVERY TARGETING INHIBITOR OF JRNL TITL 2 APOPTOSIS PROTEINS: DISCOVERY OF A NON-ALANINE LEAD SERIES JRNL TITL 3 WITH DUAL ACTIVITY AGAINST CIAP1 AND XIAP. JRNL REF J.MED.CHEM. V. 58 6574 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26218264 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00706 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 17321 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 962 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1261 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 866 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.52000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.617 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 907 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 13 ; 0.006 ; 0.036 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1230 ; 1.427 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): 26 ; 0.586 ; 1.531 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 105 ; 5.865 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;37.546 ;23.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 142 ;17.843 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;14.511 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 119 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 728 ; 0.001 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): 6 ; 0.001 ; 0.107 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): 423 ; 2.163 ; 5.332 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): 482 ; 3.146 ; 6.132 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 483 ; 3.143 ; 6.136 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): 301 ; 7.380 ;12.717 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 302 ; 7.370 ;12.728 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 : 1 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 354 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4201 -28.8005 -3.9931 REMARK 3 T TENSOR REMARK 3 T11: 0.0187 T22: 0.0667 REMARK 3 T33: 0.0258 T12: -0.0029 REMARK 3 T13: -0.0004 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 5.5400 L22: 2.6938 REMARK 3 L33: 3.5788 L12: -0.3251 REMARK 3 L13: 1.2618 L23: -0.3896 REMARK 3 S TENSOR REMARK 3 S11: 0.0810 S12: -0.4023 S13: 0.0480 REMARK 3 S21: 0.1777 S22: -0.0320 S23: 0.0659 REMARK 3 S31: -0.0979 S32: -0.0104 S33: -0.0490 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5C3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 70 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 59.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 2OPY REMARK 200 REMARK 200 REMARK: BLOCKS 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: 0.1M HEPES-NAOH 7.5, 3.9M NACL, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 52.55200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.27600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.82800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.55200 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 78.82800 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 26.27600 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: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 520 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 548 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 584 LIES ON A SPECIAL POSITION. 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 GLY A 245 REMARK 465 SER A 246 REMARK 465 HIS A 247 REMARK 465 MET A 248 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 549 O HOH A 549 5455 1.43 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 GLU A 337 -56.44 118.19 REMARK 500 GLU A 350 40.83 -76.06 REMARK 500 CYS A 351 -35.54 -159.63 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 A 662 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 663 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 664 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 665 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 666 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A 667 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH A 668 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH A 669 DISTANCE = 7.76 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 SG REMARK 620 2 CYS A 303 SG 108.2 REMARK 620 3 HIS A 320 NE2 97.6 116.5 REMARK 620 4 CYS A 327 SG 119.2 109.6 105.8 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 4XF A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C0K RELATED DB: PDB REMARK 900 SAME PROTEIN BUT WITH DIFFERENT LIGANDS. REMARK 900 RELATED ID: 5C0L RELATED DB: PDB REMARK 900 SAME PROTEIN BUT WITH DIFFERENT LIGANDS. REMARK 900 RELATED ID: 5C3H RELATED DB: PDB REMARK 900 SAME PROTEIN BUT WITH DIFFERENT LIGANDS. DBREF 5C3K A 249 354 UNP P98170 XIAP_HUMAN 249 354 SEQADV 5C3K GLY A 245 UNP P98170 EXPRESSION TAG SEQADV 5C3K SER A 246 UNP P98170 EXPRESSION TAG SEQADV 5C3K HIS A 247 UNP P98170 EXPRESSION TAG SEQADV 5C3K MET A 248 UNP P98170 EXPRESSION TAG SEQRES 1 A 110 GLY SER HIS MET ASN PHE PRO ASN SER THR ASN LEU PRO SEQRES 2 A 110 ARG ASN PRO SER MET ALA ASP TYR GLU ALA ARG ILE PHE SEQRES 3 A 110 THR PHE GLY THR TRP ILE TYR SER VAL ASN LYS GLU GLN SEQRES 4 A 110 LEU ALA ARG ALA GLY PHE TYR ALA LEU GLY GLU GLY ASP SEQRES 5 A 110 LYS VAL LYS CYS PHE HIS CYS GLY GLY GLY LEU THR ASP SEQRES 6 A 110 TRP LYS PRO SER GLU ASP PRO TRP GLU GLN HIS ALA LYS SEQRES 7 A 110 TRP TYR PRO GLY CYS LYS TYR LEU LEU GLU GLN LYS GLY SEQRES 8 A 110 GLN GLU TYR ILE ASN ASN ILE HIS LEU THR HIS SER LEU SEQRES 9 A 110 GLU GLU CYS LEU VAL ARG HET ZN A 401 1 HET 4XF A 402 26 HETNAM ZN ZINC ION HETNAM 4XF (2S)-1-[(6-AMINOPYRIDIN-2-YL)AMINO]-1-OXOPROPAN-2- HETNAM 2 4XF AMINIUM FORMUL 2 ZN ZN 2+ FORMUL 3 4XF C8 H13 N4 O 1+ FORMUL 4 HOH *169(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 GLU A 337 VAL A 353 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 SSBOND 1 CYS A 351 CYS A 351 1555 5455 2.17 LINK SG CYS A 300 ZN ZN A 401 1555 1555 2.37 LINK SG CYS A 303 ZN ZN A 401 1555 1555 2.22 LINK NE2 HIS A 320 ZN ZN A 401 1555 1555 2.15 LINK SG CYS A 327 ZN ZN A 401 1555 1555 2.38 SITE 1 AC1 4 CYS A 300 CYS A 303 HIS A 320 CYS A 327 SITE 1 AC2 9 GLY A 306 LEU A 307 THR A 308 ASP A 309 SITE 2 AC2 9 TRP A 310 GLU A 314 GLN A 319 TRP A 323 SITE 3 AC2 9 HOH A 552 CRYST1 71.616 71.616 105.104 90.00 90.00 90.00 P 41 2 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 0.013963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009514 0.00000