PDB Short entry for 5J7F HEADER LIGASE 06-APR-16 5J7F TITLE STRUCTURE OF MDM2 WITH LOW MOLECULAR WEIGHT INHIBITOR WITH ALIPHATIC TITLE 2 LINKER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,P53-BINDING COMPND 5 PROTEIN MDM2; COMPND 6 EC: 6.3.2.-; COMPND 7 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: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P53, MDM2, MDMX, PROTEIN-PROTEIN INTERACTION, CANCER, INHIBITOR, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.TWARDA-CLAPA,K.KUBICA,K.GUZIK,G.DUBIN,T.A.HOLAK REVDAT 4 10-JAN-24 5J7F 1 REMARK REVDAT 3 31-JAN-18 5J7F 1 REMARK REVDAT 2 07-JUN-17 5J7F 1 JRNL REVDAT 1 17-MAY-17 5J7F 0 JRNL AUTH A.TWARDA-CLAPA,S.KRZANIK,K.KUBICA,K.GUZIK,B.LABUZEK, JRNL AUTH 2 C.G.NEOCHORITIS,K.KHOURY,K.KOWALSKA,M.CZUB,G.DUBIN, JRNL AUTH 3 A.DOMLING,L.SKALNIAK,T.A.HOLAK JRNL TITL 1,4,5-TRISUBSTITUTED IMIDAZOLE-BASED P53-MDM2/MDMX JRNL TITL 2 ANTAGONISTS WITH ALIPHATIC LINKERS FOR CONJUGATION WITH JRNL TITL 3 BIOLOGICAL CARRIERS. JRNL REF J. MED. CHEM. V. 60 4234 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28482147 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00104 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30895 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2220 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3221 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 188 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : -1.55000 REMARK 3 B33 (A**2) : 0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.358 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3485 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3358 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4722 ; 2.151 ; 2.047 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7713 ; 0.892 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.092 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;44.571 ;24.030 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 602 ;18.319 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;22.531 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3804 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 780 ; 0.003 ; 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): 1612 ; 1.808 ; 2.305 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1611 ; 1.809 ; 2.303 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2008 ; 2.734 ; 3.436 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 111 REMARK 3 ORIGIN FOR THE GROUP (A): 38.7113 0.6698 44.9125 REMARK 3 T TENSOR REMARK 3 T11: 0.1545 T22: 0.0116 REMARK 3 T33: 0.2727 T12: -0.0263 REMARK 3 T13: 0.0049 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.2394 L22: 1.8107 REMARK 3 L33: 1.8297 L12: -0.3851 REMARK 3 L13: -0.3147 L23: -0.0708 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: 0.0040 S13: -0.0778 REMARK 3 S21: -0.0251 S22: 0.0334 S23: 0.0350 REMARK 3 S31: -0.0189 S32: -0.1041 S33: -0.0180 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 12 B 114 REMARK 3 ORIGIN FOR THE GROUP (A): 48.8524 -20.5603 50.8723 REMARK 3 T TENSOR REMARK 3 T11: 0.0634 T22: 0.0334 REMARK 3 T33: 0.3139 T12: -0.0109 REMARK 3 T13: -0.0028 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 1.1200 L22: 3.0157 REMARK 3 L33: 1.9169 L12: -0.5923 REMARK 3 L13: 0.4376 L23: -0.1523 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: -0.1279 S13: -0.0366 REMARK 3 S21: 0.0067 S22: -0.0459 S23: -0.1211 REMARK 3 S31: -0.1382 S32: 0.1026 S33: 0.0557 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 : C 11 C 111 REMARK 3 ORIGIN FOR THE GROUP (A): 62.0385 -42.7781 52.8111 REMARK 3 T TENSOR REMARK 3 T11: 0.1102 T22: 0.0099 REMARK 3 T33: 0.3263 T12: 0.0095 REMARK 3 T13: 0.0089 T23: 0.0274 REMARK 3 L TENSOR REMARK 3 L11: 1.6068 L22: 2.9713 REMARK 3 L33: 1.3779 L12: 0.4060 REMARK 3 L13: 0.2040 L23: 0.7968 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.0932 S13: 0.0435 REMARK 3 S21: 0.1606 S22: -0.0285 S23: -0.0042 REMARK 3 S31: 0.1651 S32: 0.0286 S33: 0.0144 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 : D 12 D 110 REMARK 3 ORIGIN FOR THE GROUP (A): 41.8582 21.9528 32.1997 REMARK 3 T TENSOR REMARK 3 T11: 0.2025 T22: 0.0098 REMARK 3 T33: 0.2550 T12: -0.0241 REMARK 3 T13: 0.0341 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.6881 L22: 2.3204 REMARK 3 L33: 0.9821 L12: 0.2375 REMARK 3 L13: 0.1210 L23: -0.5817 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: -0.0514 S13: 0.1191 REMARK 3 S21: 0.1145 S22: -0.0227 S23: 0.0492 REMARK 3 S31: 0.0431 S32: -0.0720 S33: 0.0143 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 5J7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL 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 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32584 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.004 REMARK 200 RESOLUTION RANGE LOW (A) : 87.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.95200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: 4HBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5 WITH 0.2 M NACL AND REMARK 280 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 87.37500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 CYS A 2 REMARK 465 ASN A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 MET A 6 REMARK 465 SER A 7 REMARK 465 VAL A 8 REMARK 465 PRO A 9 REMARK 465 THR A 10 REMARK 465 GLN A 112 REMARK 465 GLN A 113 REMARK 465 GLU A 114 REMARK 465 SER A 115 REMARK 465 SER A 116 REMARK 465 ASP A 117 REMARK 465 SER A 118 REMARK 465 GLY A 119 REMARK 465 THR A 120 REMARK 465 SER A 121 REMARK 465 VAL A 122 REMARK 465 SER A 123 REMARK 465 GLU A 124 REMARK 465 ASN A 125 REMARK 465 MET B 1 REMARK 465 CYS B 2 REMARK 465 ASN B 3 REMARK 465 THR B 4 REMARK 465 ASN B 5 REMARK 465 MET B 6 REMARK 465 SER B 7 REMARK 465 VAL B 8 REMARK 465 PRO B 9 REMARK 465 THR B 10 REMARK 465 ASP B 11 REMARK 465 SER B 115 REMARK 465 SER B 116 REMARK 465 ASP B 117 REMARK 465 SER B 118 REMARK 465 GLY B 119 REMARK 465 THR B 120 REMARK 465 SER B 121 REMARK 465 VAL B 122 REMARK 465 SER B 123 REMARK 465 GLU B 124 REMARK 465 ASN B 125 REMARK 465 MET C 1 REMARK 465 CYS C 2 REMARK 465 ASN C 3 REMARK 465 THR C 4 REMARK 465 ASN C 5 REMARK 465 MET C 6 REMARK 465 SER C 7 REMARK 465 VAL C 8 REMARK 465 PRO C 9 REMARK 465 THR C 10 REMARK 465 GLN C 112 REMARK 465 GLN C 113 REMARK 465 GLU C 114 REMARK 465 SER C 115 REMARK 465 SER C 116 REMARK 465 ASP C 117 REMARK 465 SER C 118 REMARK 465 GLY C 119 REMARK 465 THR C 120 REMARK 465 SER C 121 REMARK 465 VAL C 122 REMARK 465 SER C 123 REMARK 465 GLU C 124 REMARK 465 ASN C 125 REMARK 465 MET D 1 REMARK 465 CYS D 2 REMARK 465 ASN D 3 REMARK 465 THR D 4 REMARK 465 ASN D 5 REMARK 465 MET D 6 REMARK 465 SER D 7 REMARK 465 VAL D 8 REMARK 465 PRO D 9 REMARK 465 THR D 10 REMARK 465 ASP D 11 REMARK 465 ASN D 111 REMARK 465 GLN D 112 REMARK 465 GLN D 113 REMARK 465 GLU D 114 REMARK 465 SER D 115 REMARK 465 SER D 116 REMARK 465 ASP D 117 REMARK 465 SER D 118 REMARK 465 GLY D 119 REMARK 465 THR D 120 REMARK 465 SER D 121 REMARK 465 VAL D 122 REMARK 465 SER D 123 REMARK 465 GLU D 124 REMARK 465 ASN D 125 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 ASP A 11 CG OD1 OD2 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 ASN A 111 CG OD1 ND2 REMARK 470 SER B 17 OG REMARK 470 LYS B 51 CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 GLU B 114 CG CD OE1 OE2 REMARK 470 ASP C 11 CG OD1 OD2 REMARK 470 GLN C 44 CG CD OE1 NE2 REMARK 470 LYS C 70 CG CD CE NZ REMARK 470 LYS C 94 CE NZ REMARK 470 GLN D 44 CG CD OE1 NE2 REMARK 470 LYS D 45 CE NZ REMARK 470 LYS D 51 CD CE NZ REMARK 470 LYS D 70 CG CD CE NZ REMARK 470 VAL D 110 CG1 CG2 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 VAL B 14 CB - CA - C ANGL. DEV. = -13.3 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 GLU A 95 79.38 -110.37 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 6GG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6GG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6GG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6GG D 201 DBREF 5J7F A 1 125 UNP Q00987 MDM2_HUMAN 1 125 DBREF 5J7F B 1 125 UNP Q00987 MDM2_HUMAN 1 125 DBREF 5J7F C 1 125 UNP Q00987 MDM2_HUMAN 1 125 DBREF 5J7F D 1 125 UNP Q00987 MDM2_HUMAN 1 125 SEQRES 1 A 125 MET CYS ASN THR ASN MET SER VAL PRO THR ASP GLY ALA SEQRES 2 A 125 VAL THR THR SER GLN ILE PRO ALA SER GLU GLN GLU THR SEQRES 3 A 125 LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SEQRES 4 A 125 SER VAL GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU SEQRES 5 A 125 VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG SEQRES 6 A 125 LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER SEQRES 7 A 125 ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SEQRES 8 A 125 SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR SEQRES 9 A 125 ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SER ASP SEQRES 10 A 125 SER GLY THR SER VAL SER GLU ASN SEQRES 1 B 125 MET CYS ASN THR ASN MET SER VAL PRO THR ASP GLY ALA SEQRES 2 B 125 VAL THR THR SER GLN ILE PRO ALA SER GLU GLN GLU THR SEQRES 3 B 125 LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SEQRES 4 B 125 SER VAL GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU SEQRES 5 B 125 VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG SEQRES 6 B 125 LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER SEQRES 7 B 125 ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SEQRES 8 B 125 SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR SEQRES 9 B 125 ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SER ASP SEQRES 10 B 125 SER GLY THR SER VAL SER GLU ASN SEQRES 1 C 125 MET CYS ASN THR ASN MET SER VAL PRO THR ASP GLY ALA SEQRES 2 C 125 VAL THR THR SER GLN ILE PRO ALA SER GLU GLN GLU THR SEQRES 3 C 125 LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SEQRES 4 C 125 SER VAL GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU SEQRES 5 C 125 VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG SEQRES 6 C 125 LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER SEQRES 7 C 125 ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SEQRES 8 C 125 SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR SEQRES 9 C 125 ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SER ASP SEQRES 10 C 125 SER GLY THR SER VAL SER GLU ASN SEQRES 1 D 125 MET CYS ASN THR ASN MET SER VAL PRO THR ASP GLY ALA SEQRES 2 D 125 VAL THR THR SER GLN ILE PRO ALA SER GLU GLN GLU THR SEQRES 3 D 125 LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SEQRES 4 D 125 SER VAL GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU SEQRES 5 D 125 VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG SEQRES 6 D 125 LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER SEQRES 7 D 125 ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SEQRES 8 D 125 SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR SEQRES 9 D 125 ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SER ASP SEQRES 10 D 125 SER GLY THR SER VAL SER GLU ASN HET 6GG A 201 47 HET 6GG B 201 47 HET 6GG C 201 47 HET 6GG D 201 47 HETNAM 6GG 4-({6-[(6-CHLORO-3-{1-[(4-CHLOROPHENYL)METHYL]-4-(4- HETNAM 2 6GG FLUOROPHENYL)-1H-IMIDAZOL-5-YL}-1H-INDOLE-2-CARBONYL) HETNAM 3 6GG OXY]HEXYL}AMINO)-4-OXOBUTANOIC ACID FORMUL 5 6GG 4(C35 H33 CL2 F N4 O5) FORMUL 9 HOH *145(H2 O) HELIX 1 AA1 PRO A 20 GLU A 25 1 6 HELIX 2 AA2 LYS A 31 VAL A 41 1 11 HELIX 3 AA3 MET A 50 LYS A 64 1 15 HELIX 4 AA4 ASP A 80 GLY A 87 1 8 HELIX 5 AA5 GLU A 95 ARG A 105 1 11 HELIX 6 AA6 SER B 22 GLU B 25 5 4 HELIX 7 AA7 LYS B 31 SER B 40 1 10 HELIX 8 AA8 MET B 50 LYS B 64 1 15 HELIX 9 AA9 ASP B 80 GLY B 87 1 8 HELIX 10 AB1 GLU B 95 ARG B 105 1 11 HELIX 11 AB2 PRO C 20 GLU C 25 1 6 HELIX 12 AB3 LYS C 31 SER C 40 1 10 HELIX 13 AB4 MET C 50 LYS C 64 1 15 HELIX 14 AB5 ASP C 80 GLY C 87 1 8 HELIX 15 AB6 GLU C 95 ARG C 105 1 11 HELIX 16 AB7 PRO D 20 GLU D 25 1 6 HELIX 17 AB8 LYS D 31 SER D 40 1 10 HELIX 18 AB9 MET D 50 LYS D 64 1 15 HELIX 19 AC1 ASP D 80 GLY D 87 1 8 HELIX 20 AC2 GLU D 95 ARG D 105 1 11 SHEET 1 AA1 3 TYR A 48 THR A 49 0 SHEET 2 AA1 3 LEU A 27 PRO A 30 -1 N VAL A 28 O TYR A 48 SHEET 3 AA1 3 LEU A 107 VAL A 109 -1 O VAL A 108 N ARG A 29 SHEET 1 AA2 2 ILE A 74 TYR A 76 0 SHEET 2 AA2 2 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 SHEET 1 AA3 2 LEU B 27 VAL B 28 0 SHEET 2 AA3 2 TYR B 48 THR B 49 -1 O TYR B 48 N VAL B 28 SHEET 1 AA4 2 ILE B 74 TYR B 76 0 SHEET 2 AA4 2 SER B 90 SER B 92 -1 O PHE B 91 N VAL B 75 SHEET 1 AA5 3 TYR C 48 THR C 49 0 SHEET 2 AA5 3 LEU C 27 PRO C 30 -1 N VAL C 28 O TYR C 48 SHEET 3 AA5 3 LEU C 107 VAL C 109 -1 O VAL C 108 N ARG C 29 SHEET 1 AA6 2 ILE C 74 TYR C 76 0 SHEET 2 AA6 2 SER C 90 SER C 92 -1 O PHE C 91 N VAL C 75 SHEET 1 AA7 3 TYR D 48 THR D 49 0 SHEET 2 AA7 3 LEU D 27 PRO D 30 -1 N VAL D 28 O TYR D 48 SHEET 3 AA7 3 LEU D 107 VAL D 108 -1 O VAL D 108 N ARG D 29 SHEET 1 AA8 2 ILE D 74 TYR D 76 0 SHEET 2 AA8 2 SER D 90 SER D 92 -1 O PHE D 91 N VAL D 75 SITE 1 AC1 15 VAL A 14 LEU A 54 GLY A 58 ILE A 61 SITE 2 AC1 15 MET A 62 TYR A 67 VAL A 93 HIS A 96 SITE 3 AC1 15 ILE A 99 HOH A 322 MET D 62 TYR D 67 SITE 4 AC1 15 GLN D 72 LYS D 94 6GG D 201 SITE 1 AC2 12 VAL B 14 THR B 16 LEU B 54 GLY B 58 SITE 2 AC2 12 ILE B 61 MET B 62 TYR B 67 VAL B 93 SITE 3 AC2 12 HIS B 96 TYR C 67 GLN C 72 6GG C 201 SITE 1 AC3 14 MET B 62 TYR B 67 GLN B 72 VAL B 93 SITE 2 AC3 14 6GG B 201 VAL C 14 LEU C 54 GLY C 58 SITE 3 AC3 14 ILE C 61 MET C 62 TYR C 67 VAL C 93 SITE 4 AC3 14 HIS C 96 HOH C 303 SITE 1 AC4 15 MET A 62 TYR A 67 GLN A 72 HIS A 96 SITE 2 AC4 15 6GG A 201 VAL D 14 LEU D 54 PHE D 55 SITE 3 AC4 15 GLY D 58 ILE D 61 MET D 62 TYR D 67 SITE 4 AC4 15 GLN D 72 VAL D 93 HIS D 96 CRYST1 37.758 174.750 37.810 90.00 93.48 90.00 P 1 21 1 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 0.026484 0.000000 0.001609 0.00000 SCALE2 0.000000 0.005722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026497 0.00000