HEADER LIGASE/LIGASE INHIBITOR 02-FEB-10 3LNJ TITLE CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH D-PEPTIDE INHIBITOR TITLE 2 (DPMI-ALPHA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, C, E; COMPND 4 FRAGMENT: UNP RESIDUES 25-109, P53 BINDING DOMAIN; COMPND 5 SYNONYM: P53-BINDING PROTEIN MDM2, ONCOPROTEIN MDM2, DOUBLE MINUTE 2 COMPND 6 PROTEIN, HDM2; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: D-PEPTIDE INHIBITOR; COMPND 11 CHAIN: B, D, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: MDM2 SEQUENCE OCCURS NATURALLY IN HUMANS.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE, D-ENANTIOMER OF PHAGE-SELECTED L- SOURCE 7 PEPTIDE KEYWDS MDM2, P53 BINDING DOMAIN, D-PEPTIDE ACTIVATOR OF MDM2, MDM2-D-PEPTIDE KEYWDS 2 COMPLEX, HOST-VIRUS INTERACTION, LIGASE, METAL-BINDING, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, PROTO-ONCOGENE, UBL CONJUGATION PATHWAY, ZINC- KEYWDS 4 FINGER, LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.PAZGIER,W.LU REVDAT 7 06-NOV-24 3LNJ 1 REMARK REVDAT 6 22-NOV-23 3LNJ 1 REMARK REVDAT 5 06-SEP-23 3LNJ 1 LINK REVDAT 4 13-JUL-11 3LNJ 1 VERSN REVDAT 3 21-JUL-10 3LNJ 1 JRNL REVDAT 2 28-APR-10 3LNJ 1 JRNL REVDAT 1 09-MAR-10 3LNJ 0 JRNL AUTH M.LIU,M.PAZGIER,C.LI,W.YUAN,C.LI,W.LU JRNL TITL A LEFT-HANDED SOLUTION TO PEPTIDE INHIBITION OF THE P53-MDM2 JRNL TITL 2 INTERACTION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 49 3649 2010 JRNL REFN ISSN 1433-7851 JRNL PMID 20449836 JRNL DOI 10.1002/ANIE.201000329 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 106.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 12608 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 660 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 889 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2357 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.16000 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): 0.472 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.276 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.158 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2413 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3164 ; 1.989 ; 2.079 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 7.193 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;45.355 ;23.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;17.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.311 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1616 ; 0.010 ; 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): 1393 ; 0.853 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2178 ; 1.500 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1020 ; 2.887 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 986 ; 4.357 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 26 A 108 REMARK 3 RESIDUE RANGE : E 118 E 313 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0516 -47.2746 -6.1212 REMARK 3 T TENSOR REMARK 3 T11: 0.0531 T22: 0.0719 REMARK 3 T33: 0.0617 T12: 0.0407 REMARK 3 T13: -0.0472 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 3.0117 L22: 3.0032 REMARK 3 L33: 3.8420 L12: 0.2089 REMARK 3 L13: -0.1000 L23: -0.7569 REMARK 3 S TENSOR REMARK 3 S11: -0.1203 S12: -0.0456 S13: 0.0716 REMARK 3 S21: -0.2309 S22: 0.0303 S23: 0.1101 REMARK 3 S31: 0.0941 S32: 0.0239 S33: 0.0900 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 : C 26 C 108 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3710 -28.9169 2.9253 REMARK 3 T TENSOR REMARK 3 T11: 0.1033 T22: 0.1992 REMARK 3 T33: 0.1492 T12: -0.0605 REMARK 3 T13: -0.0677 T23: -0.0814 REMARK 3 L TENSOR REMARK 3 L11: 2.3924 L22: 4.4880 REMARK 3 L33: 3.1489 L12: -0.1708 REMARK 3 L13: -0.2656 L23: 0.5668 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: -0.3995 S13: 0.3186 REMARK 3 S21: 0.0355 S22: 0.1517 S23: -0.3897 REMARK 3 S31: -0.2846 S32: 0.6592 S33: -0.1636 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 120 C 314 REMARK 3 ORIGIN FOR THE GROUP (A): 15.1026 -8.3987 -8.7403 REMARK 3 T TENSOR REMARK 3 T11: 0.1555 T22: 0.1189 REMARK 3 T33: 0.0936 T12: 0.0140 REMARK 3 T13: -0.0222 T23: -0.0804 REMARK 3 L TENSOR REMARK 3 L11: 4.5077 L22: 4.8169 REMARK 3 L33: 3.6451 L12: 0.5048 REMARK 3 L13: -0.0067 L23: -0.5542 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: 0.2525 S13: -0.0947 REMARK 3 S21: -0.7131 S22: -0.0660 S23: -0.0839 REMARK 3 S31: 0.1677 S32: -0.3475 S33: 0.0641 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3LNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13268 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 106.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.77500 REMARK 200 R SYM FOR SHELL (I) : 0.71000 REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 3EQS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CACODYLATE TRIHYDRATE, AND 30% PEG 8000, PH 6.5., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.76800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.76800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.48800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 106.73900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.48800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 106.73900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.76800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.48800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 106.73900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 22.76800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.48800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 106.73900 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE D-PEPTIDE INHIBITOR IS OLIGOPEPTIDE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: D-PEPTIDE INHIBITOR REMARK 400 CHAIN: B, D, F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 VAL A 109 REMARK 465 DTH B 1 REMARK 465 GLU C 25 REMARK 465 VAL C 109 REMARK 465 DTH D 1 REMARK 465 GLU E 25 REMARK 465 VAL E 109 REMARK 465 DTH F 1 REMARK 465 DSG F 2 REMARK 465 DAL F 5 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 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DSG B 2 CA - C - N ANGL. DEV. = -21.2 DEGREES REMARK 500 DSG B 2 O - C - N ANGL. DEV. = -13.0 DEGREES REMARK 500 DTY B 4 O - C - N ANGL. DEV. = -10.9 DEGREES REMARK 500 DAL B 5 CA - C - N ANGL. DEV. = 18.9 DEGREES REMARK 500 DAL B 5 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 DLY B 9 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 DSG D 2 CA - C - N ANGL. DEV. = -19.1 DEGREES REMARK 500 DTR D 3 C - N - CA ANGL. DEV. = 20.2 DEGREES REMARK 500 DTY D 4 O - C - N ANGL. DEV. = 12.1 DEGREES REMARK 500 DAL D 5 O - C - N ANGL. DEV. = -11.2 DEGREES REMARK 500 DGL D 8 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 DLY D 9 O - C - N ANGL. DEV. = 15.9 DEGREES REMARK 500 DLE D 11 CA - C - N ANGL. DEV. = 14.7 DEGREES REMARK 500 DLE D 11 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 DSG F 6 CA - C - N ANGL. DEV. = 19.9 DEGREES REMARK 500 DSG F 6 O - C - N ANGL. DEV. = -20.0 DEGREES REMARK 500 DLE F 7 O - C - N ANGL. DEV. = -20.8 DEGREES REMARK 500 DGL F 8 C - N - CA ANGL. DEV. = 17.5 DEGREES REMARK 500 DAR F 12 C - N - CA ANGL. DEV. = 16.6 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 DLE F 7 44.32 23.09 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 DSG B 2 DTR B 3 -131.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 DSG B 2 29.52 REMARK 500 DTR B 3 -13.90 REMARK 500 DTY B 4 -26.25 REMARK 500 DGL B 8 14.50 REMARK 500 DLY B 9 26.52 REMARK 500 DSG D 2 22.60 REMARK 500 DAL D 5 19.66 REMARK 500 DLE D 7 19.87 REMARK 500 DGL D 8 25.37 REMARK 500 DTR F 3 -11.92 REMARK 500 DSG F 6 -24.18 REMARK 500 DLE F 7 33.96 REMARK 500 DGL F 8 17.28 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 SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL E 3968 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IWY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MDM2 COMPLEXED WITH D-PEPTIDE (12 REMARK 900 RESIDUES) REMARK 900 RELATED ID: 3EQS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MDM2 COMPLEXED WITH 12-MER PEPTIDE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 3IUX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MDM2 COMPLEXED WITH A POTENT MINIATURE REMARK 900 PROTEIN INHIBITOR (18-RESIDUES) REMARK 900 RELATED ID: 1YCR RELATED DB: PDB REMARK 900 STRUCTURE OF THE MDM2 OCOPROTEIN BOUND TO THE P53 TUMOR REMARK 900 TRANSACTIVATION DOMAIN DBREF 3LNJ A 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3LNJ B 1 12 PDB 3LNJ 3LNJ 1 12 DBREF 3LNJ C 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3LNJ D 1 12 PDB 3LNJ 3LNJ 1 12 DBREF 3LNJ E 25 109 UNP Q00987 MDM2_HUMAN 25 109 DBREF 3LNJ F 1 12 PDB 3LNJ 3LNJ 1 12 SEQRES 1 A 85 GLU THR LEU VAL ARG PRO LYS PRO LEU 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 12 DTH DSG DTR DTY DAL DSG DLE DGL DLY DLE DLE DAR SEQRES 1 C 85 GLU THR LEU VAL ARG PRO LYS PRO LEU 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 12 DTH DSG DTR DTY DAL DSG DLE DGL DLY DLE DLE DAR SEQRES 1 E 85 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 2 E 85 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 3 E 85 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 4 E 85 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 5 E 85 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 6 E 85 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 7 E 85 ILE TYR ARG ASN LEU VAL VAL SEQRES 1 F 12 DTH DSG DTR DTY DAL DSG DLE DGL DLY DLE DLE DAR HET DSG B 2 8 HET DTR B 3 14 HET DTY B 4 12 HET DAL B 5 5 HET DSG B 6 8 HET DLE B 7 8 HET DGL B 8 9 HET DLY B 9 9 HET DLE B 10 8 HET DLE B 11 8 HET DAR B 12 12 HET DSG D 2 8 HET DTR D 3 14 HET DTY D 4 12 HET DAL D 5 5 HET DSG D 6 8 HET DLE D 7 8 HET DGL D 8 9 HET DLY D 9 9 HET DLE D 10 8 HET DLE D 11 8 HET DAR D 12 12 HET DTR F 3 14 HET DTY F 4 12 HET DSG F 6 8 HET DLE F 7 8 HET DGL F 8 9 HET DLY F 9 9 HET DLE F 10 8 HET DLE F 11 8 HET DAR F 12 12 HET SO4 A 201 5 HET CL C 201 1 HET GOL E 201 6 HETNAM DSG D-ASPARAGINE HETNAM DTR D-TRYPTOPHAN HETNAM DTY D-TYROSINE HETNAM DAL D-ALANINE HETNAM DLE D-LEUCINE HETNAM DGL D-GLUTAMIC ACID HETNAM DLY D-LYSINE HETNAM DAR D-ARGININE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DSG 5(C4 H8 N2 O3) FORMUL 2 DTR 3(C11 H12 N2 O2) FORMUL 2 DTY 3(C9 H11 N O3) FORMUL 2 DAL 2(C3 H7 N O2) FORMUL 2 DLE 9(C6 H13 N O2) FORMUL 2 DGL 3(C5 H9 N O4) FORMUL 2 DLY 3(C6 H14 N2 O2) FORMUL 2 DAR 3(C6 H15 N4 O2 1+) FORMUL 7 SO4 O4 S 2- FORMUL 8 CL CL 1- FORMUL 9 GOL C3 H8 O3 FORMUL 10 HOH *61(H2 O) HELIX 1 1 LYS A 31 SER A 40 1 10 HELIX 2 2 THR A 49 ARG A 65 1 17 HELIX 3 3 ASP A 80 GLY A 87 1 8 HELIX 4 4 GLU A 95 ASN A 106 1 12 HELIX 5 13 DTY B 4 DAR B 12 1 9 HELIX 6 5 LYS C 31 SER C 40 1 10 HELIX 7 6 THR C 49 ARG C 65 1 17 HELIX 8 7 ASP C 80 GLY C 87 1 8 HELIX 9 8 GLU C 95 ARG C 105 1 11 HELIX 10 14 DTY D 4 DAR D 12 1 9 HELIX 11 9 LYS E 31 SER E 40 1 10 HELIX 12 10 THR E 49 LYS E 64 1 16 HELIX 13 11 ASP E 80 GLY E 87 1 8 HELIX 14 12 GLU E 95 ASN E 106 1 12 HELIX 15 15 DSG F 6 DAR F 12 1 7 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 ARG C 29 PRO C 30 0 SHEET 2 B 2 LEU C 107 VAL C 108 -1 O VAL C 108 N ARG C 29 SHEET 1 C 2 ILE C 74 TYR C 76 0 SHEET 2 C 2 SER C 90 SER C 92 -1 O PHE C 91 N VAL C 75 SHEET 1 D 2 ILE E 74 TYR E 76 0 SHEET 2 D 2 SER E 90 SER E 92 -1 O PHE E 91 N VAL E 75 LINK C DSG B 2 N DTR B 3 1555 1555 1.43 LINK C DTR B 3 N DTY B 4 1555 1555 1.30 LINK C DTY B 4 N DAL B 5 1555 1555 1.26 LINK C DAL B 5 N DSG B 6 1555 1555 1.27 LINK C DSG B 6 N DLE B 7 1555 1555 1.28 LINK C DLE B 7 N DGL B 8 1555 1555 1.27 LINK C DGL B 8 N DLY B 9 1555 1555 1.26 LINK C DLY B 9 N DLE B 10 1555 1555 1.29 LINK C DLE B 10 N DLE B 11 1555 1555 1.27 LINK C DLE B 11 N DAR B 12 1555 1555 1.30 LINK C DSG D 2 N DTR D 3 1555 1555 1.42 LINK C DTR D 3 N DTY D 4 1555 1555 1.28 LINK C DTY D 4 N DAL D 5 1555 1555 1.29 LINK C DAL D 5 N DSG D 6 1555 1555 1.27 LINK C DSG D 6 N DLE D 7 1555 1555 1.27 LINK C DLE D 7 N DGL D 8 1555 1555 1.29 LINK C DGL D 8 N DLY D 9 1555 1555 1.26 LINK C DLY D 9 N DLE D 10 1555 1555 1.30 LINK C DLE D 10 N DLE D 11 1555 1555 1.28 LINK C DLE D 11 N DAR D 12 1555 1555 1.27 LINK C DTR F 3 N DTY F 4 1555 1555 1.29 LINK C DSG F 6 N DLE F 7 1555 1555 1.28 LINK C DLE F 7 N DGL F 8 1555 1555 1.28 LINK C DGL F 8 N DLY F 9 1555 1555 1.27 LINK C DLY F 9 N DLE F 10 1555 1555 1.27 LINK C DLE F 10 N DLE F 11 1555 1555 1.26 LINK C DLE F 11 N DAR F 12 1555 1555 1.28 SITE 1 AC1 3 HIS A 73 GLY A 87 ARG A 105 SITE 1 AC2 2 LYS A 64 LYS C 51 SITE 1 AC3 3 THR E 26 ARG E 97 THR E 101 CRYST1 68.976 213.478 45.536 90.00 90.00 90.00 C 2 2 21 24 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 0.014498 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021961 0.00000