HEADER LIGASE 21-APR-15 4ZFI TITLE STRUCTURE OF MDM2 WITH LOW MOLECULAR WEIGHT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 18-113; COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,P53-BINDING COMPND 6 PROTEIN MDM2; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: P53 BINDING DOMAIN OF MDM2 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-20 KEYWDS P53-BINDING PROTEIN MDM2, ONCOPROTEIN MDM2, DOUBLE MINUTE 2 PROTEIN, KEYWDS 2 HDM2, SMALL MOLECULE INHIBITOR, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.ZAK,A.TWARDA-CLAPA,E.M.WRONA,P.GRUDNIK,G.DUBIN,T.A.HOLAK REVDAT 3 10-JAN-24 4ZFI 1 REMARK REVDAT 2 28-DEC-16 4ZFI 1 JRNL REVDAT 1 19-OCT-16 4ZFI 0 JRNL AUTH E.SURMIAK,A.TWARDA-CLAPA,K.M.ZAK,B.MUSIELAK,M.D.TOMALA, JRNL AUTH 2 K.KUBICA,P.GRUDNIK,M.MADEJ,M.JABLONSKI,J.POTEMPA, JRNL AUTH 3 J.KALINOWSKA-TLUSCIK,A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL A UNIQUE MDM2-BINDING MODE OF THE 3-PYRROLIN-2-ONE- AND JRNL TITL 2 2-FURANONE-BASED ANTAGONISTS OF THE P53-MDM2 INTERACTION. JRNL REF ACS CHEM. BIOL. V. 11 3310 2016 JRNL REFN ESSN 1554-8937 JRNL PMID 27709883 JRNL DOI 10.1021/ACSCHEMBIO.6B00596 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29436 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1564 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) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.91000 REMARK 3 B22 (A**2) : 3.58000 REMARK 3 B33 (A**2) : -2.67000 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): 0.187 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.235 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3178 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3012 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4332 ; 2.159 ; 2.040 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6883 ; 1.535 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 6.366 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;43.325 ;23.739 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 530 ;14.217 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.775 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 489 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3467 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 717 ; 0.008 ; 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): 1506 ; 2.250 ; 2.496 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1505 ; 2.229 ; 2.494 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1875 ; 3.108 ; 3.721 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 18 111 B 18 111 5591 0.060 0.050 REMARK 3 2 A 18 109 C 18 109 5172 0.140 0.050 REMARK 3 3 A 19 110 D 19 110 4934 0.130 0.050 REMARK 3 4 B 18 109 C 18 109 5041 0.140 0.050 REMARK 3 5 B 19 110 D 19 110 4904 0.130 0.050 REMARK 3 6 C 19 109 D 19 109 5004 0.110 0.050 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 18 A 112 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7632 0.4711 21.8971 REMARK 3 T TENSOR REMARK 3 T11: 0.0208 T22: 0.0216 REMARK 3 T33: 0.0089 T12: 0.0136 REMARK 3 T13: 0.0056 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.3917 L22: 0.4028 REMARK 3 L33: 0.7284 L12: -0.0958 REMARK 3 L13: -0.2027 L23: 0.0910 REMARK 3 S TENSOR REMARK 3 S11: 0.0430 S12: 0.0070 S13: 0.0244 REMARK 3 S21: -0.0200 S22: -0.0247 S23: -0.0392 REMARK 3 S31: -0.0114 S32: -0.0674 S33: -0.0183 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 17 B 113 REMARK 3 ORIGIN FOR THE GROUP (A): -9.3494 0.2062 5.2326 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0176 REMARK 3 T33: 0.0154 T12: -0.0026 REMARK 3 T13: 0.0055 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.5300 L22: 0.4081 REMARK 3 L33: 1.2982 L12: 0.0720 REMARK 3 L13: -0.3901 L23: 0.0258 REMARK 3 S TENSOR REMARK 3 S11: 0.0404 S12: -0.0069 S13: 0.0350 REMARK 3 S21: 0.0251 S22: 0.0090 S23: 0.0430 REMARK 3 S31: 0.0165 S32: 0.0630 S33: -0.0494 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 18 C 110 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4903 4.4420 30.8574 REMARK 3 T TENSOR REMARK 3 T11: 0.0187 T22: 0.0080 REMARK 3 T33: 0.0251 T12: 0.0048 REMARK 3 T13: 0.0125 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.3756 L22: 0.3503 REMARK 3 L33: 0.9685 L12: 0.0809 REMARK 3 L13: -0.0461 L23: 0.2444 REMARK 3 S TENSOR REMARK 3 S11: 0.0184 S12: 0.0291 S13: -0.0201 REMARK 3 S21: 0.0043 S22: 0.0074 S23: -0.0115 REMARK 3 S31: -0.0352 S32: -0.0323 S33: -0.0258 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 19 D 111 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4777 4.5399 -3.9116 REMARK 3 T TENSOR REMARK 3 T11: 0.0099 T22: 0.0047 REMARK 3 T33: 0.0162 T12: -0.0032 REMARK 3 T13: 0.0124 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.4730 L22: 0.5910 REMARK 3 L33: 1.1753 L12: -0.0030 REMARK 3 L13: 0.1830 L23: -0.1825 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: -0.0077 S13: -0.0206 REMARK 3 S21: 0.0173 S22: 0.0201 S23: 0.0186 REMARK 3 S31: -0.0274 S32: 0.0464 S33: -0.0113 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 4ZFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31037 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 56.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3800 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.610 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: 3LBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.2 M SODIUM REMARK 280 CHLORIDE, 25% (W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 33.18000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.12500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 17 REMARK 465 GLN A 113 REMARK 465 MET C 17 REMARK 465 ASN C 111 REMARK 465 GLN C 112 REMARK 465 GLN C 113 REMARK 465 MET D 17 REMARK 465 GLN D 18 REMARK 465 GLN D 112 REMARK 465 GLN D 113 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 31 CE NZ REMARK 470 LYS A 36 CE NZ REMARK 470 LYS A 51 CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 GLN A 71 NE2 REMARK 470 ASN A 79 CG OD1 ND2 REMARK 470 LYS A 94 CE NZ REMARK 470 LYS A 98 NZ REMARK 470 ARG A 105 NE CZ NH1 NH2 REMARK 470 MET B 17 CG SD CE REMARK 470 GLU B 25 CD OE1 OE2 REMARK 470 LEU B 33 CD1 CD2 REMARK 470 LYS B 36 CD CE NZ REMARK 470 LYS B 39 NZ REMARK 470 LYS B 51 CE NZ REMARK 470 MET B 62 CG SD CE REMARK 470 ARG B 65 NE CZ NH1 NH2 REMARK 470 GLU B 69 CG CD OE1 OE2 REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 GLN B 71 CG CD OE1 NE2 REMARK 470 GLN B 72 CG CD OE1 NE2 REMARK 470 LYS B 94 NZ REMARK 470 LYS B 98 NZ REMARK 470 GLN B 113 C O CG CD OE1 NE2 REMARK 470 PRO C 20 O REMARK 470 GLU C 25 OE1 OE2 REMARK 470 LYS C 31 NZ REMARK 470 LYS C 36 NZ REMARK 470 ASP C 46 CG OD1 OD2 REMARK 470 LYS C 51 CE NZ REMARK 470 GLU C 69 CB CG CD OE1 OE2 REMARK 470 LYS C 70 CB CG CD CE NZ REMARK 470 GLN C 71 CB CG CD OE1 NE2 REMARK 470 GLN C 72 CD OE1 NE2 REMARK 470 LYS C 94 CD CE NZ REMARK 470 ILE D 19 CG1 CD1 REMARK 470 GLU D 25 OE2 REMARK 470 LYS D 31 NZ REMARK 470 LYS D 36 CG CD CE NZ REMARK 470 LYS D 51 CE NZ REMARK 470 MET D 62 CG SD CE REMARK 470 ARG D 65 CD NE CZ NH1 NH2 REMARK 470 GLU D 69 CG CD OE1 OE2 REMARK 470 LYS D 70 O CB CG CD CE NZ REMARK 470 GLN D 71 CG CD OE1 NE2 REMARK 470 GLN D 72 CG CD OE1 NE2 REMARK 470 LYS D 94 CD CE NZ REMARK 470 GLU D 95 CD OE1 OE2 REMARK 470 ARG D 97 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 111 CG OD1 ND2 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 ND2 ASN C 106 O HOH C 301 1.46 REMARK 500 O HOH B 346 O HOH B 360 1.98 REMARK 500 O HOH A 381 O HOH A 386 2.11 REMARK 500 O HOH C 321 O HOH C 374 2.13 REMARK 500 OH TYR D 104 O HOH D 301 2.17 REMARK 500 O HOH B 370 O HOH B 372 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 B 342 O HOH D 341 4455 2.17 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 LYS D 70 -69.96 90.80 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 373 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH B 374 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH D 369 DISTANCE = 6.35 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4NJ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4NJ B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4NJ C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4NJ D 201 DBREF 4ZFI A 18 113 UNP Q00987 MDM2_HUMAN 24 119 DBREF 4ZFI B 18 113 UNP Q00987 MDM2_HUMAN 24 119 DBREF 4ZFI C 18 113 UNP Q00987 MDM2_HUMAN 24 119 DBREF 4ZFI D 18 113 UNP Q00987 MDM2_HUMAN 24 119 SEQADV 4ZFI MET A 17 UNP Q00987 INITIATING METHIONINE SEQADV 4ZFI MET B 17 UNP Q00987 INITIATING METHIONINE SEQADV 4ZFI MET C 17 UNP Q00987 INITIATING METHIONINE SEQADV 4ZFI MET D 17 UNP Q00987 INITIATING METHIONINE SEQRES 1 A 97 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 A 97 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 A 97 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 A 97 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 A 97 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 A 97 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 A 97 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 A 97 VAL VAL VAL ASN GLN GLN SEQRES 1 B 97 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 B 97 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 B 97 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 B 97 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 B 97 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 B 97 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 B 97 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 B 97 VAL VAL VAL ASN GLN GLN SEQRES 1 C 97 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 C 97 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 C 97 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 C 97 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 C 97 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 C 97 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 C 97 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 C 97 VAL VAL VAL ASN GLN GLN SEQRES 1 D 97 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 D 97 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 D 97 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 D 97 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 D 97 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 D 97 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 D 97 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 D 97 VAL VAL VAL ASN GLN GLN HET 4NJ A 201 34 HET 4NJ B 201 34 HET 4NJ C 201 34 HET 4NJ D 201 34 HETNAM 4NJ (5S)-3,5-BIS(4-CHLOROBENZYL)-4-(6-CHLORO-1H-INDOL-3- HETNAM 2 4NJ YL)-5-HYDROXY-1-METHYL-1,5-DIHYDRO-2H-PYRROL-2-ONE FORMUL 5 4NJ 4(C27 H21 CL3 N2 O2) FORMUL 9 HOH *313(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 PRO B 20 GLU B 25 1 6 HELIX 7 AA7 LYS B 31 VAL B 41 1 11 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 LYS C 31 VAL C 41 1 11 HELIX 12 AB3 MET C 50 LYS C 64 1 15 HELIX 13 AB4 ASP C 80 GLY C 87 1 8 HELIX 14 AB5 GLU C 95 ARG C 105 1 11 HELIX 15 AB6 PRO D 20 GLU D 25 1 6 HELIX 16 AB7 LYS D 31 VAL D 41 1 11 HELIX 17 AB8 MET D 50 LYS D 64 1 15 HELIX 18 AB9 ASP D 80 GLY D 87 1 8 HELIX 19 AC1 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 3 TYR B 48 THR B 49 0 SHEET 2 AA3 3 LEU B 27 PRO B 30 -1 N VAL B 28 O TYR B 48 SHEET 3 AA3 3 LEU B 107 VAL B 109 -1 O VAL B 108 N ARG B 29 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 109 -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 14 LEU A 54 PHE A 55 GLY A 58 ILE A 61 SITE 2 AC1 14 TYR A 67 VAL A 93 HIS A 96 ILE A 99 SITE 3 AC1 14 TYR A 100 HOH A 309 HOH A 322 HOH A 329 SITE 4 AC1 14 HOH A 331 LYS D 51 SITE 1 AC2 12 LEU B 54 PHE B 55 GLY B 58 ILE B 61 SITE 2 AC2 12 TYR B 67 HIS B 96 ILE B 99 HOH B 310 SITE 3 AC2 12 HOH B 312 HOH B 327 HOH B 334 LYS C 51 SITE 1 AC3 11 LYS B 51 LEU C 54 PHE C 55 GLY C 58 SITE 2 AC3 11 TYR C 67 HIS C 96 ILE C 99 TYR C 100 SITE 3 AC3 11 HOH C 305 HOH C 311 HOH C 326 SITE 1 AC4 12 LYS A 51 LEU D 54 PHE D 55 GLY D 58 SITE 2 AC4 12 TYR D 67 VAL D 93 HIS D 96 ILE D 99 SITE 3 AC4 12 HOH D 306 HOH D 314 HOH D 321 HOH D 343 CRYST1 66.360 70.250 96.440 90.00 90.00 90.00 P 21 21 21 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 0.015069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010369 0.00000