HEADER LIGASE/LIGASE ACTIVATOR 02-JAN-12 3VBG TITLE STRUCTURE OF HDM2 WITH DIMER INDUCING INDOLYL HYDANTOIN RO-2443 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 25-109; 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: HUMAN; SOURCE 6 GENE: MDM2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE40 KEYWDS LIGASE, MDM2, MDMX, P53, LIGASE-LIGASE ACTIVATOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.M.LUKACS,C.A.JANSON,B.J.GRAVES REVDAT 5 13-SEP-23 3VBG 1 REMARK SEQADV REVDAT 4 17-JUL-19 3VBG 1 REMARK REVDAT 3 01-AUG-12 3VBG 1 JRNL REVDAT 2 25-JUL-12 3VBG 1 JRNL REVDAT 1 27-JUN-12 3VBG 0 JRNL AUTH B.GRAVES,T.THOMPSON,M.XIA,C.JANSON,C.LUKACS,D.DEO, JRNL AUTH 2 P.DI LELLO,D.FRY,C.GARVIE,K.S.HUANG,L.GAO,C.TOVAR,A.LOVEY, JRNL AUTH 3 J.WANNER,L.T.VASSILEV JRNL TITL ACTIVATION OF THE P53 PATHWAY BY SMALL-MOLECULE-INDUCED MDM2 JRNL TITL 2 AND MDMX DIMERIZATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 11788 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22745160 JRNL DOI 10.1073/PNAS.1203789109 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18025 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 992 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1246 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 112 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -67.84000 REMARK 3 B22 (A**2) : -67.84000 REMARK 3 B33 (A**2) : 135.67000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2990 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4044 ; 2.808 ; 2.043 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 9.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;42.754 ;23.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;25.025 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.807 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2192 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 4 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.252 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.239 REMARK 3 TWIN DOMAIN : 3 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.252 REMARK 3 TWIN DOMAIN : 4 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.257 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 26 A 109 REMARK 3 RESIDUE RANGE : A 1 A 1 REMARK 3 RESIDUE RANGE : A 2 A 14 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0891 -14.9949 -18.9170 REMARK 3 T TENSOR REMARK 3 T11: 0.3705 T22: 0.2705 REMARK 3 T33: 0.0267 T12: 0.0559 REMARK 3 T13: -0.0006 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 1.2693 L22: 1.3954 REMARK 3 L33: 1.5097 L12: -0.1442 REMARK 3 L13: 0.0729 L23: 0.1097 REMARK 3 S TENSOR REMARK 3 S11: 0.0028 S12: 0.0513 S13: -0.0742 REMARK 3 S21: -0.1029 S22: -0.1677 S23: 0.0681 REMARK 3 S31: -0.2031 S32: -0.0936 S33: 0.1649 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 25 B 109 REMARK 3 RESIDUE RANGE : B 1 B 1 REMARK 3 RESIDUE RANGE : B 3 B 18 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2076 -22.5382 4.2577 REMARK 3 T TENSOR REMARK 3 T11: 0.3939 T22: 0.2367 REMARK 3 T33: 0.0473 T12: -0.0733 REMARK 3 T13: 0.0156 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.5528 L22: 1.4383 REMARK 3 L33: 1.1115 L12: 0.1802 REMARK 3 L13: 0.0541 L23: 0.1981 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.0979 S13: 0.1736 REMARK 3 S21: 0.1783 S22: -0.2050 S23: -0.0039 REMARK 3 S31: 0.1601 S32: -0.0592 S33: 0.1751 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 26 C 109 REMARK 3 RESIDUE RANGE : C 1 C 1 REMARK 3 RESIDUE RANGE : C 4 C 4 REMARK 3 RESIDUE RANGE : C 110 C 110 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5647 -36.9182 -46.9260 REMARK 3 T TENSOR REMARK 3 T11: 0.2103 T22: 0.4370 REMARK 3 T33: 0.0237 T12: 0.0153 REMARK 3 T13: 0.0302 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 0.3712 L22: 0.5239 REMARK 3 L33: 1.3128 L12: -0.2731 REMARK 3 L13: 0.5825 L23: -0.0987 REMARK 3 S TENSOR REMARK 3 S11: -0.0841 S12: -0.0065 S13: 0.0282 REMARK 3 S21: 0.0301 S22: -0.0448 S23: 0.0407 REMARK 3 S31: -0.0777 S32: -0.1534 S33: 0.1289 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 25 D 109 REMARK 3 RESIDUE RANGE : D 1 D 1 REMARK 3 RESIDUE RANGE : D 7 D 19 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1836 -40.4838 -23.6301 REMARK 3 T TENSOR REMARK 3 T11: 0.3525 T22: 0.2680 REMARK 3 T33: 0.0287 T12: 0.0780 REMARK 3 T13: 0.0022 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.0602 L22: 1.1079 REMARK 3 L33: 1.0258 L12: -0.0553 REMARK 3 L13: -0.2737 L23: -0.2150 REMARK 3 S TENSOR REMARK 3 S11: -0.1403 S12: -0.0065 S13: 0.0521 REMARK 3 S21: 0.2090 S22: 0.0365 S23: 0.0748 REMARK 3 S31: 0.0898 S32: 0.0150 S33: 0.1038 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: NULL REMARK 4 REMARK 4 3VBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1RV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 54% SATURATED AMMONIUM SULFATE, 0.1M REMARK 280 TRIS, 5% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.72467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.86233 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLU A 25 REMARK 465 GLU C 25 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O VAL A 28 O ASP A 46 2.10 REMARK 500 O LEU D 37 OG SER D 40 2.11 REMARK 500 O ILE D 99 CG1 ILE D 103 2.11 REMARK 500 O TYR B 104 N ASN B 106 2.12 REMARK 500 N LYS D 31 O ASN D 106 2.14 REMARK 500 NH1 ARG D 65 OH TYR D 67 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 VAL A 109 N GLU D 25 1565 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 96 CG HIS A 96 CD2 0.054 REMARK 500 HIS C 73 CG HIS C 73 CD2 0.057 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 27 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 PRO A 30 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 LEU B 37 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU B 54 CA - CB - CG ANGL. DEV. = 18.4 DEGREES REMARK 500 PRO C 32 C - N - CA ANGL. DEV. = 10.7 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 LYS A 31 155.54 -45.34 REMARK 500 GLN A 44 22.36 -156.36 REMARK 500 LYS A 45 -150.06 -122.73 REMARK 500 ASP A 46 -10.33 -149.50 REMARK 500 ARG A 65 51.34 23.65 REMARK 500 ASN A 79 -33.03 108.77 REMARK 500 ARG A 105 8.05 -69.47 REMARK 500 VAL A 108 -11.63 -45.93 REMARK 500 THR B 26 87.36 -155.37 REMARK 500 GLU B 33 -78.02 -72.84 REMARK 500 LEU B 34 -81.94 -24.64 REMARK 500 LEU B 35 -48.01 -29.63 REMARK 500 ALA B 43 161.21 -35.02 REMARK 500 GLN B 44 -66.44 -128.60 REMARK 500 LYS B 45 152.26 -36.75 REMARK 500 ILE B 61 -37.68 -33.72 REMARK 500 MET B 62 -70.87 -75.23 REMARK 500 LYS B 64 33.60 -79.84 REMARK 500 ARG B 65 84.07 8.82 REMARK 500 ASN B 79 -29.35 91.60 REMARK 500 PHE B 91 156.13 176.42 REMARK 500 LYS B 94 -71.50 -54.73 REMARK 500 GLU B 95 106.97 -43.46 REMARK 500 ARG B 105 -20.11 -34.08 REMARK 500 LYS C 31 113.82 -38.52 REMARK 500 MET C 50 21.25 -65.88 REMARK 500 LEU C 66 7.90 -65.50 REMARK 500 GLU C 69 -54.27 -26.83 REMARK 500 SER C 78 141.91 -38.98 REMARK 500 ASN C 79 -51.35 75.64 REMARK 500 ASP C 84 -72.51 -63.79 REMARK 500 PHE C 91 140.06 156.27 REMARK 500 HIS C 96 -68.06 -19.83 REMARK 500 ARG C 97 -81.49 -28.01 REMARK 500 TYR C 104 -72.47 -44.31 REMARK 500 ARG C 105 -19.26 -34.48 REMARK 500 GLU D 33 -71.15 -50.11 REMARK 500 GLN D 44 20.75 -177.02 REMARK 500 TYR D 48 155.64 177.94 REMARK 500 LYS D 51 18.48 -60.10 REMARK 500 PHE D 55 -76.50 -72.42 REMARK 500 ARG D 65 49.74 82.33 REMARK 500 ASP D 68 156.06 -47.50 REMARK 500 LYS D 70 -75.56 -71.65 REMARK 500 GLN D 71 97.15 -66.98 REMARK 500 SER D 78 117.74 -31.67 REMARK 500 ASN D 79 74.89 55.53 REMARK 500 SER D 90 139.07 162.99 REMARK 500 VAL D 93 -16.77 -45.65 REMARK 500 GLU D 95 67.54 -50.23 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU D 107 VAL D 108 149.38 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 03M A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U15 RELATED DB: PDB REMARK 900 RELATED ID: 1RV1 RELATED DB: PDB DBREF 3VBG A 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3VBG B 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3VBG C 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3VBG D 25 109 UNP Q00987 MDM2_HUMAN 25 109 SEQADV 3VBG GLU A 33 UNP Q00987 LEU 33 ENGINEERED MUTATION SEQADV 3VBG GLU B 33 UNP Q00987 LEU 33 ENGINEERED MUTATION SEQADV 3VBG GLU C 33 UNP Q00987 LEU 33 ENGINEERED MUTATION SEQADV 3VBG GLU D 33 UNP Q00987 LEU 33 ENGINEERED MUTATION SEQRES 1 A 85 GLU THR LEU VAL ARG PRO LYS PRO GLU LEU LEU LYS LEU SEQRES 2 A 85 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 3 A 85 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 4 A 85 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 5 A 85 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 6 A 85 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 7 A 85 ILE TYR ARG ASN LEU VAL VAL SEQRES 1 B 85 GLU THR LEU VAL ARG PRO LYS PRO GLU LEU LEU LYS LEU SEQRES 2 B 85 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 3 B 85 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 4 B 85 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 5 B 85 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 6 B 85 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 7 B 85 ILE TYR ARG ASN LEU VAL VAL SEQRES 1 C 85 GLU THR LEU VAL ARG PRO LYS PRO GLU LEU LEU LYS LEU SEQRES 2 C 85 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 3 C 85 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 4 C 85 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 5 C 85 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 6 C 85 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 7 C 85 ILE TYR ARG ASN LEU VAL VAL SEQRES 1 D 85 GLU THR LEU VAL ARG PRO LYS PRO GLU LEU LEU LYS LEU SEQRES 2 D 85 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 3 D 85 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 4 D 85 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 5 D 85 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 6 D 85 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 7 D 85 ILE TYR ARG ASN LEU VAL VAL HET 03M A 1 28 HET 03M B 1 28 HET 03M C 1 28 HET 03M D 1 28 HETNAM 03M (5Z)-5-[(6-CHLORO-7-METHYL-1H-INDOL-3-YL)METHYLIDENE]- HETNAM 2 03M 3-(3,4-DIFLUOROBENZYL)IMIDAZOLIDINE-2,4-DIONE FORMUL 5 03M 4(C20 H14 CL F2 N3 O2) FORMUL 9 HOH *19(H2 O) HELIX 1 1 LYS A 31 VAL A 41 1 11 HELIX 2 2 THR A 49 LYS A 64 1 16 HELIX 3 3 ASP A 80 GLY A 87 1 8 HELIX 4 4 GLU A 95 ARG A 105 1 11 HELIX 5 5 LYS B 31 VAL B 41 1 11 HELIX 6 6 MET B 50 LYS B 64 1 15 HELIX 7 7 ASP B 80 GLY B 87 1 8 HELIX 8 8 GLU B 95 ASN B 106 1 12 HELIX 9 9 PRO C 32 LYS C 39 1 8 HELIX 10 10 LYS C 51 LYS C 64 1 14 HELIX 11 11 ASP C 80 GLY C 87 1 8 HELIX 12 12 GLU C 95 ARG C 105 1 11 HELIX 13 13 LYS D 31 LYS D 39 1 9 HELIX 14 14 THR D 49 ARG D 65 1 17 HELIX 15 15 ASP D 80 GLY D 87 1 8 HELIX 16 16 GLU D 95 TYR D 104 1 10 SHEET 1 A 2 ILE A 74 TYR A 76 0 SHEET 2 A 2 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 SHEET 1 B 2 LEU B 27 VAL B 28 0 SHEET 2 B 2 TYR B 48 THR B 49 -1 O TYR B 48 N VAL B 28 SHEET 1 C 2 ILE B 74 TYR B 76 0 SHEET 2 C 2 SER B 90 SER B 92 -1 O PHE B 91 N VAL B 75 SHEET 1 D 2 ILE C 74 TYR C 76 0 SHEET 2 D 2 SER C 90 SER C 92 -1 O PHE C 91 N VAL C 75 SHEET 1 E 2 ARG D 29 PRO D 30 0 SHEET 2 E 2 LEU D 107 VAL D 108 -1 O VAL D 108 N ARG D 29 SHEET 1 F 2 ILE D 74 VAL D 75 0 SHEET 2 F 2 PHE D 91 SER D 92 -1 O PHE D 91 N VAL D 75 SITE 1 AC1 11 MET A 62 ARG A 65 TYR A 67 GLN A 72 SITE 2 AC1 11 VAL A 93 03M B 1 LEU B 54 LEU B 57 SITE 3 AC1 11 GLY B 58 VAL B 93 ILE B 99 SITE 1 AC2 11 03M A 1 LEU A 54 LEU A 57 GLY A 58 SITE 2 AC2 11 VAL A 93 ILE A 99 GLY B 58 ILE B 61 SITE 3 AC2 11 MET B 62 TYR B 67 GLN B 72 SITE 1 AC3 10 TYR C 67 GLU C 69 GLN C 72 03M D 1 SITE 2 AC3 10 LEU D 54 LEU D 57 GLY D 58 ILE D 61 SITE 3 AC3 10 VAL D 93 ILE D 99 SITE 1 AC4 10 03M C 1 LEU C 54 LEU C 57 VAL C 93 SITE 2 AC4 10 ILE C 99 ILE D 61 MET D 62 ARG D 65 SITE 3 AC4 10 TYR D 67 GLN D 72 CRYST1 64.392 64.392 167.587 90.00 90.00 120.00 P 32 12 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 0.015530 0.008966 0.000000 0.00000 SCALE2 0.000000 0.017932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005967 0.00000