HEADER LIGASE 29-APR-04 1T4F TITLE STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH AN OPTIMIZED P53 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-PROTEIN LIGASE E3 MDM2; COMPND 3 CHAIN: M; COMPND 4 SYNONYM: P53-BINDING PROTEIN MDM2, ONCOPROTEIN MDM2, DOUBLE MINUTE 2 COMPND 5 PROTEIN, HDM2; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: OPTIMIZED P53 PEPTIDE; COMPND 11 CHAIN: P; COMPND 12 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX4T-3; SOURCE 10 MOL_ID: 2 KEYWDS MDM2-P53 PEPTIDE COMPLEX, P53-BINDING PROTEIN MDM2 ONCOPROTEIN MDM2 KEYWDS 2 DOUBLE MINUTE 2 PROTEIN HDM2, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR B.L.GRASBERGER,C.SCHUBERT,H.K.KOBLISH,T.E.CARVER,C.F.FRANKS,S.Y.ZHAO, AUTHOR 2 T.LU,L.V.LAFRANCE,D.J.PARKS REVDAT 4 23-AUG-23 1T4F 1 REMARK SEQADV REVDAT 3 24-FEB-09 1T4F 1 VERSN REVDAT 2 12-APR-05 1T4F 1 JRNL REVDAT 1 08-FEB-05 1T4F 0 JRNL AUTH B.L.GRASBERGER,T.LU,C.SCHUBERT,D.J.PARKS,T.E.CARVER, JRNL AUTH 2 H.K.KOBLISH,M.D.CUMMINGS,L.V.LAFRANCE,K.L.MILKIEWICZ JRNL TITL DISCOVERY AND COCRYSTAL STRUCTURE OF BENZODIAZEPINEDIONE JRNL TITL 2 HDM2 ANTAGONISTS THAT ACTIVATE P53 IN CELLS JRNL REF J.MED.CHEM. V. 48 909 2005 JRNL REFN ISSN 0022-2623 JRNL PMID 15715460 JRNL DOI 10.1021/JM049137G REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MOLECULAR REMARK 3 : SIMULATIONS (BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 849537.540 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.1 REMARK 3 NUMBER OF REFLECTIONS : 7246 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 786 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7246 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 729 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.61000 REMARK 3 B22 (A**2) : -3.31000 REMARK 3 B33 (A**2) : 0.70000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 47.50 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.07200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX 2000.1 REMARK 200 STARTING MODEL: 1YCR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, BICINE, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 20.51500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.51500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.79500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, P 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 GLY M 16 REMARK 465 SER M 17 REMARK 465 GLN M 18 REMARK 465 ILE M 19 REMARK 465 PRO M 20 REMARK 465 ALA M 21 REMARK 465 SER M 22 REMARK 465 ASN M 111 REMARK 465 GLN M 112 REMARK 465 GLN M 113 REMARK 465 GLU M 114 REMARK 465 SER M 115 REMARK 465 SER M 116 REMARK 465 ASP M 117 REMARK 465 SER M 118 REMARK 465 GLY M 119 REMARK 465 THR M 120 REMARK 465 SER M 121 REMARK 465 VAL M 122 REMARK 465 SER M 123 REMARK 465 GLU M 124 REMARK 465 ASN M 125 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 GLN M 71 72.03 -159.63 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 M 126 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T4E RELATED DB: PDB REMARK 900 SAME PROTEIN, SHORTER CLONE, IN COMPLEX WITH A SMALL MOLECULE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1YCR RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT CLONE, IN COMPLEX WITH A WT P53 PEPTIDE REMARK 900 RELATED ID: 1RV1 RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT CLONE, IN COMPLEX WITH A SMALL MOLECULE REMARK 900 INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR INDICATED THAT CHAIN P WAS DERIVED REMARK 999 FROM A PHAGE DISPLAY EXPERIMENT,THEREFORE REMARK 999 THERE ARE NO MATCHES IN THE SEQUENCE DATABASE DBREF 1T4F M 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 1T4F P 18 26 PDB 1T4F 1T4F 18 26 SEQADV 1T4F GLY M 16 UNP Q00987 CLONING ARTIFACT SEQRES 1 M 110 GLY SER GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL SEQRES 2 M 110 ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL SEQRES 3 M 110 GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU SEQRES 4 M 110 PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR SEQRES 5 M 110 ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP SEQRES 6 M 110 LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL SEQRES 7 M 110 LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN SEQRES 8 M 110 LEU VAL VAL VAL ASN GLN GLN GLU SER SER ASP SER GLY SEQRES 9 M 110 THR SER VAL SER GLU ASN SEQRES 1 P 9 ARG PHE MET ASP TYR TRP GLU GLY LEU HET SO4 M 126 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *59(H2 O) HELIX 1 1 LYS M 31 GLY M 42 1 12 HELIX 2 2 MET M 50 LYS M 64 1 15 HELIX 3 3 ASP M 80 GLY M 87 1 8 HELIX 4 4 GLU M 95 ARG M 105 1 11 HELIX 5 5 ARG P 18 GLU P 24 1 7 SHEET 1 A 3 TYR M 48 THR M 49 0 SHEET 2 A 3 LEU M 27 PRO M 30 -1 N VAL M 28 O TYR M 48 SHEET 3 A 3 LEU M 107 VAL M 110 -1 O VAL M 110 N LEU M 27 SHEET 1 B 3 TYR M 67 ASP M 68 0 SHEET 2 B 3 GLN M 71 TYR M 76 -1 O ILE M 74 N ASP M 68 SHEET 3 B 3 SER M 90 SER M 92 -1 O PHE M 91 N VAL M 75 SITE 1 AC1 4 GLU M 23 GLN M 24 LYS M 70 ARG M 105 CRYST1 41.030 43.590 54.570 90.00 90.00 90.00 P 21 21 21 4 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 0.024372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018325 0.00000