HEADER CELL CYCLE 17-DEC-09 2X0V TITLE STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 4- TITLE 2 (TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, RESIDUES 94-312; COMPND 5 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13, COMPND 6 P53; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL CYCLE, HOST-VIRUS INTERACTION, TRANSCRIPTION REGULATION, KEYWDS 2 TRANSCRIPTION FACTOR, LI-FRAUMENI DRUG DISCOVERY, SURFACE CREVICE, KEYWDS 3 TUMOR SUPPRESSOR, PROTEIN STABILIZATION, TRANSCRIPTION, METAL KEYWDS 4 BINDING, CANCER, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR N.BASSE,J.L.KAAR,A.C.JOERGER,A.R.FERSHT REVDAT 4 20-DEC-23 2X0V 1 REMARK LINK REVDAT 3 08-MAY-19 2X0V 1 REMARK REVDAT 2 23-FEB-10 2X0V 1 KEYWDS JRNL REMARK REVDAT 1 26-JAN-10 2X0V 0 JRNL AUTH N.BASSE,J.L.KAAR,G.SETTANNI,A.C.JOERGER,T.J.RUTHERFORD, JRNL AUTH 2 A.R.FERSHT JRNL TITL TOWARD THE RATIONAL DESIGN OF P53-STABILIZING DRUGS: PROBING JRNL TITL 2 THE SURFACE OF THE ONCOGENIC Y220C MUTANT. JRNL REF CHEM.BIOL. V. 17 46 2010 JRNL REFN ISSN 1074-5521 JRNL PMID 20142040 JRNL DOI 10.1016/J.CHEMBIOL.2009.12.011 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.C.JOERGER,H.C.ANG,A.R.FERSHT REMARK 1 TITL STRUCTURAL BASIS FOR UNDERSTANDING ONCOGENIC P53 MUTATIONS REMARK 1 TITL 2 AND DESIGNING RESCUE DRUGS. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 103 15056 2006 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 17015838 REMARK 1 DOI 10.1073/PNAS.0607286103 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 86003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.0325 - 5.5706 0.95 2688 115 0.1995 0.2023 REMARK 3 2 5.5706 - 4.4306 0.98 2732 125 0.1451 0.1454 REMARK 3 3 4.4306 - 3.8732 0.98 2736 122 0.1414 0.1245 REMARK 3 4 3.8732 - 3.5202 0.99 2751 144 0.1447 0.1658 REMARK 3 5 3.5202 - 3.2686 0.99 2724 159 0.1388 0.1652 REMARK 3 6 3.2686 - 3.0763 0.99 2804 117 0.1467 0.1608 REMARK 3 7 3.0763 - 2.9225 0.99 2724 148 0.1397 0.1565 REMARK 3 8 2.9225 - 2.7955 0.99 2780 126 0.1582 0.1633 REMARK 3 9 2.7955 - 2.6880 0.99 2688 160 0.1570 0.2215 REMARK 3 10 2.6880 - 2.5954 0.99 2748 147 0.1597 0.1833 REMARK 3 11 2.5954 - 2.5143 0.99 2772 130 0.1590 0.1986 REMARK 3 12 2.5143 - 2.4425 0.99 2734 144 0.1560 0.2290 REMARK 3 13 2.4425 - 2.3783 0.99 2765 146 0.1498 0.1787 REMARK 3 14 2.3783 - 2.3203 0.98 2748 125 0.1528 0.1650 REMARK 3 15 2.3203 - 2.2676 0.98 2702 147 0.1481 0.1765 REMARK 3 16 2.2676 - 2.2193 0.99 2780 122 0.1534 0.1557 REMARK 3 17 2.2193 - 2.1750 0.98 2718 160 0.1430 0.1902 REMARK 3 18 2.1750 - 2.1340 0.98 2708 142 0.1573 0.2007 REMARK 3 19 2.1340 - 2.0959 0.99 2706 166 0.1606 0.1891 REMARK 3 20 2.0959 - 2.0604 0.97 2707 170 0.1657 0.2222 REMARK 3 21 2.0604 - 2.0272 0.99 2728 119 0.1634 0.1939 REMARK 3 22 2.0272 - 1.9960 0.97 2753 140 0.1711 0.1846 REMARK 3 23 1.9960 - 1.9666 0.98 2713 107 0.1735 0.1739 REMARK 3 24 1.9666 - 1.9389 0.97 2741 154 0.1732 0.2163 REMARK 3 25 1.9389 - 1.9128 0.98 2671 151 0.1651 0.1805 REMARK 3 26 1.9128 - 1.8879 0.97 2744 126 0.1773 0.2333 REMARK 3 27 1.8879 - 1.8643 0.98 2686 161 0.1840 0.2170 REMARK 3 28 1.8643 - 1.8419 0.97 2685 154 0.1915 0.2250 REMARK 3 29 1.8419 - 1.8205 0.98 2655 179 0.2027 0.2491 REMARK 3 30 1.8205 - 1.8000 0.94 2636 170 0.2057 0.2746 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 50.27 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.31560 REMARK 3 B22 (A**2) : -3.29170 REMARK 3 B33 (A**2) : -2.02380 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 3183 REMARK 3 ANGLE : 0.904 4326 REMARK 3 CHIRALITY : 0.065 480 REMARK 3 PLANARITY : 0.004 563 REMARK 3 DIHEDRAL : 13.611 1197 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2X0V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1290042112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2J1X REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROP VAPOR DIFFUSION AT 21 REMARK 280 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM REMARK 280 PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM REMARK 280 HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED REMARK 280 SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM REMARK 280 SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM REMARK 280 KCL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 32.61300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.69450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.54400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.69450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.61300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.54400 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU REMARK 400 ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 220 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 239 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 268 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN B, MET 133 TO LEU REMARK 400 ENGINEERED RESIDUE IN CHAIN B, VAL 203 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, TYR 220 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 239 TO TYR REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 268 TO ASP 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 SER A 94 REMARK 465 SER A 95 REMARK 465 GLU A 221 REMARK 465 PRO A 222 REMARK 465 LYS A 291 REMARK 465 LYS A 292 REMARK 465 GLY A 293 REMARK 465 GLU A 294 REMARK 465 PRO A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 465 GLU A 298 REMARK 465 LEU A 299 REMARK 465 PRO A 300 REMARK 465 PRO A 301 REMARK 465 GLY A 302 REMARK 465 SER A 303 REMARK 465 THR A 304 REMARK 465 LYS A 305 REMARK 465 ARG A 306 REMARK 465 ALA A 307 REMARK 465 LEU A 308 REMARK 465 PRO A 309 REMARK 465 ASN A 310 REMARK 465 ASN A 311 REMARK 465 THR A 312 REMARK 465 SER B 94 REMARK 465 ARG B 290 REMARK 465 LYS B 291 REMARK 465 LYS B 292 REMARK 465 GLY B 293 REMARK 465 GLU B 294 REMARK 465 PRO B 295 REMARK 465 HIS B 296 REMARK 465 HIS B 297 REMARK 465 GLU B 298 REMARK 465 LEU B 299 REMARK 465 PRO B 300 REMARK 465 PRO B 301 REMARK 465 GLY B 302 REMARK 465 SER B 303 REMARK 465 THR B 304 REMARK 465 LYS B 305 REMARK 465 ARG B 306 REMARK 465 ALA B 307 REMARK 465 LEU B 308 REMARK 465 PRO B 309 REMARK 465 ASN B 310 REMARK 465 ASN B 311 REMARK 465 THR B 312 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 ARG A 248 -1.40 76.07 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 B2071 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B2095 DISTANCE = 5.86 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 106.7 REMARK 620 3 CYS A 238 SG 110.4 107.6 REMARK 620 4 CYS A 242 SG 108.9 106.3 116.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 176 SG REMARK 620 2 HIS B 179 ND1 102.5 REMARK 620 3 CYS B 238 SG 111.7 108.3 REMARK 620 4 CYS B 242 SG 111.5 106.7 115.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X0V B 1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X0V B 1291 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BIQ RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT T123A-M133L- H168R-V203A-N239Y-R249S- REMARK 900 N268D REMARK 900 RELATED ID: 1DT7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF REMARK 900 P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB) REMARK 900 RELATED ID: 2J1X RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- Y220C-N239Y-N268D REMARK 900 RELATED ID: 1UOL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN P53 CORE DOMAIN MUTANT M133L/V203A/ REMARK 900 N239Y/N268D AT 1 .9 A RESOLUTION. REMARK 900 RELATED ID: 2B3G RELATED DB: PDB REMARK 900 P53N (FRAGMENT 33-60) BOUND TO RPA70N REMARK 900 RELATED ID: 2FOJ RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCURE OF THE N-TERMINAL DOMAIN OF HAUSP/ REMARK 900 USP7COMPLEXED WITH P53 PEPTIDE 364-367 REMARK 900 RELATED ID: 2BIN RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-H168R- V203A-N239Y-N268D REMARK 900 RELATED ID: 1OLH RELATED DB: PDB REMARK 900 P53 (OLIGOMERIZATION DOMAIN) (NMR, 35 STRUCTURES) REMARK 900 RELATED ID: 1PES RELATED DB: PDB REMARK 900 TUMOR ANTIGEN P53 (TETRAMERIZATION DOMAIN) ( P53TET) (NMR, REMARK 900 MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 1TSR RELATED DB: PDB REMARK 900 P53 CORE DOMAIN IN COMPLEX WITH DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 2J21 RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R282W REMARK 900 RELATED ID: 2GS0 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE COMPLEX BETWEEN THE PH DOMAIN OF THETFB1 REMARK 900 SUBUNIT FROM TFIIH AND THE ACTIVATION DOMAIN OF P53 REMARK 900 RELATED ID: 2J0Z RELATED DB: PDB REMARK 900 P53 TETRAMERIZATION DOMAIN WILD TYPE REMARK 900 RELATED ID: 1C26 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P53 TETRAMERIZATION DOMAIN REMARK 900 RELATED ID: 1SAL RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES) REMARK 900 RELATED ID: 1KZY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 53BP1 BRCT REGION COMPLEXED TOTUMOR REMARK 900 SUPPRESSOR P53 REMARK 900 RELATED ID: 1XQH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF THEMETHYLTRANSFERASE SET9 REMARK 900 (ALSO KNOWN AS SET7 /9) WITH A P53PEPTIDE AND SAH REMARK 900 RELATED ID: 2FEJ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN P53 DNA BINDING DOMAIN. REMARK 900 RELATED ID: 2AHI RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX III) REMARK 900 RELATED ID: 1A1U RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE DETERMINATION OF A P53 MUTANT DIMERIZATION REMARK 900 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 3SAK RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES) REMARK 900 RELATED ID: 2WGX RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- Y236F-N239Y-T253I-N268D REMARK 900 RELATED ID: 1SAF RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES) REMARK 900 RELATED ID: 2FOO RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCURE OF THE N-TERMINAL DOMAIN OF HAUSP/ REMARK 900 USP7COMPLEXED WITH P53 PEPTIDE 359-362 REMARK 900 RELATED ID: 2BIO RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-R249S-N268D REMARK 900 RELATED ID: 1OLG RELATED DB: PDB REMARK 900 P53 (OLIGOMERIZATION DOMAIN) (NMR, MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 2J11 RELATED DB: PDB REMARK 900 P53 TETRAMERIZATION DOMAIN MUTANT Y327S T329G Q331G REMARK 900 RELATED ID: 2BIP RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-H168R- V203A-N239Y-R249S-N268D REMARK 900 RELATED ID: 1PET RELATED DB: PDB REMARK 900 TUMOR ANTIGEN P53 (TETRAMERIZATION DOMAIN) ( P53TET) (NMR, 19 REMARK 900 STRUCTURES) REMARK 900 RELATED ID: 1JSP RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CBP BROMODOMAIN IN COMPLEX WITH P53 PEPTIDE REMARK 900 RELATED ID: 2J1Y RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-G245S-N268D REMARK 900 RELATED ID: 1MA3 RELATED DB: PDB REMARK 900 STRUCTURE OF A SIR2 ENZYME BOUND TO AN ACETYLATED P53PEPTIDE REMARK 900 RELATED ID: 2VUK RELATED DB: PDB REMARK 900 STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO THE REMARK 900 STABILIZING SMALL- MOLECULE DRUG PHIKAN083 REMARK 900 RELATED ID: 1AIE RELATED DB: PDB REMARK 900 P53 TETRAMERIZATION DOMAIN CRYSTAL STRUCTURE REMARK 900 RELATED ID: 2H1L RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE ONCOPROTEIN SV40 LARGE T ANTIGEN ANDP53 TUMOR REMARK 900 SUPPRESSOR COMPLEX REMARK 900 RELATED ID: 1SAJ RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES) REMARK 900 RELATED ID: 1TUP RELATED DB: PDB REMARK 900 TUMOR SUPPRESSOR P53 COMPLEXED WITH DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1HS5 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF DESIGNED P53 DIMER REMARK 900 RELATED ID: 2ATA RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX II) REMARK 900 RELATED ID: 1YCQ RELATED DB: PDB REMARK 900 XENOPUS LAEVIS MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF HUMAN P53 REMARK 900 RELATED ID: 1GZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BRCT DOMAINS OF HUMAN 53BP1 BOUND TO THE REMARK 900 P53 TUMOR SUPRESSOR REMARK 900 RELATED ID: 1SAH RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES) REMARK 900 RELATED ID: 1YCR RELATED DB: PDB REMARK 900 MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53 REMARK 900 RELATED ID: 2BIM RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R273H REMARK 900 RELATED ID: 2J10 RELATED DB: PDB REMARK 900 P53 TETRAMERIZATION DOMAIN MUTANT T329F Q331K REMARK 900 RELATED ID: 1SAK RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES) REMARK 900 RELATED ID: 2ADY RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX IV) REMARK 900 RELATED ID: 2J1Z RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-F270L REMARK 900 RELATED ID: 1SAE RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES) REMARK 900 RELATED ID: 2AC0 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX I) REMARK 900 RELATED ID: 1YCS RELATED DB: PDB REMARK 900 P53-53BP2 COMPLEX REMARK 900 RELATED ID: 2J20 RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R273C REMARK 900 RELATED ID: 1H26 RELATED DB: PDB REMARK 900 CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM REMARK 900 P53 REMARK 900 RELATED ID: 2J1W RELATED DB: PDB REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V143A- V203A-N239Y-N268D REMARK 900 RELATED ID: 2X0W RELATED DB: PDB REMARK 900 STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 5,6- REMARK 900 DIMETHOXY-2- METHYLBENZOTHIAZOLE REMARK 900 RELATED ID: 2X0U RELATED DB: PDB REMARK 900 STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO A 2-AMINO REMARK 900 SUBSTITUTED BENZOTHIAZOLE SCAFFOLD DBREF 2X0V A 94 312 UNP P04637 P53_HUMAN 94 312 DBREF 2X0V B 94 312 UNP P04637 P53_HUMAN 94 312 SEQADV 2X0V LEU A 133 UNP P04637 MET 133 ENGINEERED MUTATION SEQADV 2X0V ALA A 203 UNP P04637 VAL 203 ENGINEERED MUTATION SEQADV 2X0V CYS A 220 UNP P04637 TYR 220 ENGINEERED MUTATION SEQADV 2X0V TYR A 239 UNP P04637 ASN 239 ENGINEERED MUTATION SEQADV 2X0V ASP A 268 UNP P04637 ASN 268 ENGINEERED MUTATION SEQADV 2X0V LEU B 133 UNP P04637 MET 133 ENGINEERED MUTATION SEQADV 2X0V ALA B 203 UNP P04637 VAL 203 ENGINEERED MUTATION SEQADV 2X0V CYS B 220 UNP P04637 TYR 220 ENGINEERED MUTATION SEQADV 2X0V TYR B 239 UNP P04637 ASN 239 ENGINEERED MUTATION SEQADV 2X0V ASP B 268 UNP P04637 ASN 268 ENGINEERED MUTATION SEQRES 1 A 219 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 A 219 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 A 219 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 A 219 LEU PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 A 219 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 A 219 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 A 219 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 A 219 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 A 219 GLU GLY ASN LEU ARG ALA GLU TYR LEU ASP ASP ARG ASN SEQRES 10 A 219 THR PHE ARG HIS SER VAL VAL VAL PRO CYS GLU PRO PRO SEQRES 11 A 219 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 A 219 MET CYS TYR SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 A 219 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 A 219 ASN LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL CYS SEQRES 15 A 219 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 A 219 LEU ARG LYS LYS GLY GLU PRO HIS HIS GLU LEU PRO PRO SEQRES 17 A 219 GLY SER THR LYS ARG ALA LEU PRO ASN ASN THR SEQRES 1 B 219 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 B 219 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 B 219 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 B 219 LEU PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 B 219 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 B 219 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 B 219 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 B 219 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 B 219 GLU GLY ASN LEU ARG ALA GLU TYR LEU ASP ASP ARG ASN SEQRES 10 B 219 THR PHE ARG HIS SER VAL VAL VAL PRO CYS GLU PRO PRO SEQRES 11 B 219 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 B 219 MET CYS TYR SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 B 219 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 B 219 ASN LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL CYS SEQRES 15 B 219 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 B 219 LEU ARG LYS LYS GLY GLU PRO HIS HIS GLU LEU PRO PRO SEQRES 17 B 219 GLY SER THR LYS ARG ALA LEU PRO ASN ASN THR HET ZN A1300 1 HET X0V B1290 12 HET X0V B1291 12 HET ZN B1300 1 HETNAM ZN ZINC ION HETNAM X0V 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 X0V 2(C7 H7 F3 N2) FORMUL 7 HOH *572(H2 O) HELIX 1 1 GLN A 165 MET A 169 5 5 HELIX 2 2 HIS A 178 CYS A 182 5 5 HELIX 3 3 CYS A 277 ARG A 290 1 14 HELIX 4 4 HIS B 178 CYS B 182 5 5 HELIX 5 5 CYS B 277 LEU B 289 1 13 SHEET 1 AA 4 ARG A 110 GLY A 112 0 SHEET 2 AA 4 CYS A 141 TRP A 146 -1 O GLN A 144 N GLY A 112 SHEET 3 AA 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 AA 4 ILE A 195 VAL A 197 -1 O ARG A 196 N ASN A 235 SHEET 1 AB 7 CYS A 124 SER A 127 0 SHEET 2 AB 7 LYS A 132 CYS A 135 -1 O LYS A 132 N SER A 127 SHEET 3 AB 7 LEU A 264 VAL A 274 1 O GLU A 271 N LEU A 133 SHEET 4 AB 7 ILE A 251 GLU A 258 -1 O ILE A 251 N VAL A 272 SHEET 5 AB 7 ARG A 156 TYR A 163 -1 O ARG A 156 N GLU A 258 SHEET 6 AB 7 HIS A 214 PRO A 219 -1 O VAL A 216 N ALA A 159 SHEET 7 AB 7 GLU A 204 ASP A 207 -1 O GLU A 204 N VAL A 217 SHEET 1 BA 4 ARG B 110 GLY B 112 0 SHEET 2 BA 4 CYS B 141 TRP B 146 -1 O GLN B 144 N GLY B 112 SHEET 3 BA 4 THR B 230 TYR B 236 -1 O THR B 230 N LEU B 145 SHEET 4 BA 4 ILE B 195 VAL B 197 -1 O ARG B 196 N ASN B 235 SHEET 1 BB 7 CYS B 124 SER B 127 0 SHEET 2 BB 7 LYS B 132 CYS B 135 -1 O LYS B 132 N SER B 127 SHEET 3 BB 7 LEU B 264 VAL B 274 1 O GLU B 271 N LEU B 133 SHEET 4 BB 7 ILE B 251 GLU B 258 -1 O ILE B 251 N VAL B 272 SHEET 5 BB 7 ARG B 156 TYR B 163 -1 O ARG B 156 N GLU B 258 SHEET 6 BB 7 HIS B 214 PRO B 219 -1 O VAL B 216 N ALA B 159 SHEET 7 BB 7 GLU B 204 ASP B 207 -1 O GLU B 204 N VAL B 217 LINK SG CYS A 176 ZN ZN A1300 1555 1555 2.42 LINK ND1 HIS A 179 ZN ZN A1300 1555 1555 2.04 LINK SG CYS A 238 ZN ZN A1300 1555 1555 2.33 LINK SG CYS A 242 ZN ZN A1300 1555 1555 2.33 LINK SG CYS B 176 ZN ZN B1300 1555 1555 2.36 LINK ND1 HIS B 179 ZN ZN B1300 1555 1555 2.09 LINK SG CYS B 238 ZN ZN B1300 1555 1555 2.38 LINK SG CYS B 242 ZN ZN B1300 1555 1555 2.32 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 SITE 1 AC2 4 CYS B 176 HIS B 179 CYS B 238 CYS B 242 SITE 1 AC3 10 THR B 150 PRO B 151 PRO B 152 THR B 155 SITE 2 AC3 10 CYS B 220 GLU B 221 PRO B 222 X0V B1291 SITE 3 AC3 10 HOH B2283 HOH B2284 SITE 1 AC4 10 LEU B 145 VAL B 147 PRO B 151 CYS B 220 SITE 2 AC4 10 GLU B 221 PRO B 223 CYS B 229 THR B 230 SITE 3 AC4 10 X0V B1290 HOH B2285 CRYST1 65.226 71.088 105.389 90.00 90.00 90.00 P 21 21 21 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 0.015331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009489 0.00000