PDB Short entry for 3KMD HEADER DNA BINDING PROTEIN/DNA 10-NOV-09 3KMD TITLE CRYSTAL STRUCTURE OF THE P53 CORE DOMAIN BOUND TO A FULL CONSENSUS TITLE 2 SITE AS A SELF-ASSEMBLED TETRAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B, D, C; COMPND 4 FRAGMENT: UNP RESIDUES 92-291, DNA BINDING DOMAIN; COMPND 5 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP COMPND 8 *C)-3'; COMPND 9 CHAIN: E, F; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS P53 CORE DOMAIN, PROTEIN-DNA INTERACTION, SELF ASSEMBLED TETRAMER, KEYWDS 2 ACTIVATOR, APOPTOSIS, CELL CYCLE, DISEASE MUTATION, DNA-BINDING, KEYWDS 3 ENDOPLASMIC RETICULUM, GLYCOPROTEIN, HOST-VIRUS INTERACTION, KEYWDS 4 ISOPEPTIDE BOND, LI-FRAUMENI SYNDROME, METAL-BINDING, METHYLATION, KEYWDS 5 NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION REGULATION, KEYWDS 6 TUMOR SUPPRESSOR, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,R.DEY,L.CHEN REVDAT 4 06-SEP-23 3KMD 1 REMARK LINK REVDAT 3 01-NOV-17 3KMD 1 REMARK REVDAT 2 21-MAR-12 3KMD 1 JRNL VERSN REVDAT 1 23-FEB-10 3KMD 0 JRNL AUTH Y.CHEN,R.DEY,L.CHEN JRNL TITL CRYSTAL STRUCTURE OF THE P53 CORE DOMAIN BOUND TO A FULL JRNL TITL 2 CONSENSUS SITE AS A SELF-ASSEMBLED TETRAMER. JRNL REF STRUCTURE V. 18 246 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20159469 JRNL DOI 10.1016/J.STR.2009.11.011 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2525 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 48.5287 - 5.6318 0.99 2744 172 0.2084 0.2405 REMARK 3 2 5.6318 - 4.4712 1.00 2635 169 0.1917 0.2029 REMARK 3 3 4.4712 - 3.9063 1.00 2633 128 0.1899 0.1929 REMARK 3 4 3.9063 - 3.5492 1.00 2619 139 0.1933 0.2319 REMARK 3 5 3.5492 - 3.2949 1.00 2623 120 0.1941 0.1987 REMARK 3 6 3.2949 - 3.1007 1.00 2581 136 0.2020 0.2457 REMARK 3 7 3.1007 - 2.9454 1.00 2603 146 0.2235 0.2175 REMARK 3 8 2.9454 - 2.8172 1.00 2541 168 0.2282 0.2596 REMARK 3 9 2.8172 - 2.7088 1.00 2546 136 0.2161 0.2320 REMARK 3 10 2.7088 - 2.6153 1.00 2604 129 0.2211 0.2630 REMARK 3 11 2.6153 - 2.5335 1.00 2558 145 0.2284 0.2776 REMARK 3 12 2.5335 - 2.4611 1.00 2570 139 0.2289 0.2641 REMARK 3 13 2.4611 - 2.3963 1.00 2581 126 0.2276 0.2786 REMARK 3 14 2.3963 - 2.3379 1.00 2567 121 0.2344 0.2675 REMARK 3 15 2.3379 - 2.2847 1.00 2568 120 0.2341 0.2435 REMARK 3 16 2.2847 - 2.2361 1.00 2555 132 0.2400 0.2736 REMARK 3 17 2.2361 - 2.1914 1.00 2566 135 0.2391 0.2719 REMARK 3 18 2.1914 - 2.1500 0.99 2501 164 0.2556 0.2770 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 : 0.36 REMARK 3 B_SOL : 47.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.95100 REMARK 3 B22 (A**2) : -7.97900 REMARK 3 B33 (A**2) : 5.02800 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 : 0.006 7298 REMARK 3 ANGLE : 1.034 10052 REMARK 3 CHIRALITY : 0.064 1098 REMARK 3 PLANARITY : 0.004 1190 REMARK 3 DIHEDRAL : 18.958 2800 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 SELECTION : CHAIN B AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 ATOM PAIRS NUMBER : 1388 REMARK 3 RMSD : 0.039 REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN A AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 SELECTION : CHAIN C AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 ATOM PAIRS NUMBER : 1388 REMARK 3 RMSD : 0.040 REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: CHAIN A AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 SELECTION : CHAIN D AND NOT ((RESID 118:123) OR REMARK 3 (RESID 176) OR (RESID 179) OR (RESID 223: REMARK 3 229) OR (RESID 238) OR (RESID 242) OR REMARK 3 (RESID 248) OR (RESID 257:264)) REMARK 3 ATOM PAIRS NUMBER : 1388 REMARK 3 RMSD : 0.047 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.68 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2AC0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 142MM NACL, PH 6.68, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 32.54200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.78500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.78500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.54200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.85650 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C, 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 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 DC E 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA E 5 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES REMARK 500 DG E 13 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 DG E 13 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA E 15 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DT E 16 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC F 4 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DA F 5 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT F 6 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT F 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG F 13 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG F 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA F 15 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DT F 16 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG F 17 O4' - C1' - N9 ANGL. DEV. = 1.9 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 120 -53.93 29.77 REMARK 500 SER C 121 -10.69 99.48 REMARK 500 SER C 260 -83.39 34.91 REMARK 500 REMARK 500 REMARK: NULL 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 A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 103.1 REMARK 620 3 CYS A 238 SG 108.4 106.6 REMARK 620 4 CYS A 242 SG 115.5 106.1 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 176 SG REMARK 620 2 HIS B 179 ND1 104.3 REMARK 620 3 CYS B 238 SG 110.6 110.9 REMARK 620 4 CYS B 242 SG 116.0 100.2 113.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 176 SG REMARK 620 2 HIS D 179 ND1 99.9 REMARK 620 3 CYS D 238 SG 108.9 113.4 REMARK 620 4 CYS D 242 SG 116.3 104.7 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 176 SG REMARK 620 2 HIS C 179 ND1 102.6 REMARK 620 3 CYS C 238 SG 109.0 108.3 REMARK 620 4 CYS C 242 SG 114.3 106.8 114.9 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1 DBREF 3KMD A 92 291 UNP P04637 P53_HUMAN 92 291 DBREF 3KMD B 92 291 UNP P04637 P53_HUMAN 92 291 DBREF 3KMD D 92 291 UNP P04637 P53_HUMAN 92 291 DBREF 3KMD C 92 291 UNP P04637 P53_HUMAN 92 291 DBREF 3KMD E 1 19 PDB 3KMD 3KMD 1 19 DBREF 3KMD F 1 19 PDB 3KMD 3KMD 1 19 SEQRES 1 A 200 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 A 200 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 A 200 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 A 200 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 A 200 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 A 200 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 A 200 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 A 200 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 A 200 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 A 200 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 A 200 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 A 200 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 A 200 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 A 200 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 A 200 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 A 200 GLU ASN LEU ARG LYS SEQRES 1 B 200 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 B 200 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 B 200 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 B 200 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 B 200 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 B 200 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 B 200 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 B 200 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 B 200 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 B 200 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 B 200 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 B 200 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 B 200 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 B 200 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 B 200 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 B 200 GLU ASN LEU ARG LYS SEQRES 1 D 200 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 D 200 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 D 200 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 D 200 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 D 200 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 D 200 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 D 200 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 D 200 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 D 200 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 D 200 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 D 200 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 D 200 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 D 200 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 D 200 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 D 200 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 D 200 GLU ASN LEU ARG LYS SEQRES 1 C 200 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 C 200 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 C 200 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 C 200 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 C 200 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 C 200 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 C 200 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 C 200 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 C 200 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 C 200 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 C 200 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 C 200 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 C 200 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 C 200 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 C 200 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 C 200 GLU ASN LEU ARG LYS SEQRES 1 E 19 DG DG DG DC DA DT DG DC DC DT DA DG DG SEQRES 2 E 19 DC DA DT DG DC DC SEQRES 1 F 19 DG DG DG DC DA DT DG DC DC DT DA DG DG SEQRES 2 F 19 DC DA DT DG DC DC HET ZN A 1 1 HET ZN B 1 1 HET ZN D 1 1 HET ZN C 1 1 HETNAM ZN ZINC ION FORMUL 7 ZN 4(ZN 2+) FORMUL 11 HOH *523(H2 O) HELIX 1 1 GLN A 165 MET A 169 5 5 HELIX 2 2 CYS A 176 CYS A 182 1 7 HELIX 3 3 CYS A 277 ASN A 288 1 12 HELIX 4 4 LEU A 289 LYS A 291 5 3 HELIX 5 5 GLN B 165 MET B 169 5 5 HELIX 6 6 CYS B 176 CYS B 182 1 7 HELIX 7 7 CYS B 277 ASN B 288 1 12 HELIX 8 8 LEU B 289 LYS B 291 5 3 HELIX 9 9 GLN D 165 MET D 169 5 5 HELIX 10 10 CYS D 176 CYS D 182 1 7 HELIX 11 11 CYS D 277 ASN D 288 1 12 HELIX 12 12 LEU D 289 LYS D 291 5 3 HELIX 13 13 GLN C 165 MET C 169 5 5 HELIX 14 14 CYS C 176 CYS C 182 1 7 HELIX 15 15 CYS C 277 LEU C 289 1 13 SHEET 1 A 4 ARG A 110 GLY A 112 0 SHEET 2 A 4 CYS A 141 TRP A 146 -1 O TRP A 146 N ARG A 110 SHEET 3 A 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 A 4 ILE A 195 VAL A 197 -1 N ARG A 196 O ASN A 235 SHEET 1 B 7 CYS A 124 SER A 127 0 SHEET 2 B 7 LYS A 132 CYS A 135 -1 O PHE A 134 N THR A 125 SHEET 3 B 7 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 4 B 7 ILE A 251 GLU A 258 -1 N LEU A 257 O LEU A 265 SHEET 5 B 7 ARG A 156 TYR A 163 -1 N MET A 160 O ILE A 254 SHEET 6 B 7 HIS A 214 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 7 B 7 GLU A 204 ASP A 207 -1 N LEU A 206 O SER A 215 SHEET 1 C 4 ARG B 110 GLY B 112 0 SHEET 2 C 4 CYS B 141 TRP B 146 -1 O TRP B 146 N ARG B 110 SHEET 3 C 4 THR B 230 TYR B 236 -1 O THR B 230 N LEU B 145 SHEET 4 C 4 ILE B 195 VAL B 197 -1 N ARG B 196 O ASN B 235 SHEET 1 D 7 CYS B 124 SER B 127 0 SHEET 2 D 7 LYS B 132 CYS B 135 -1 O PHE B 134 N THR B 125 SHEET 3 D 7 LEU B 264 VAL B 274 1 O GLU B 271 N MET B 133 SHEET 4 D 7 ILE B 251 GLU B 258 -1 N THR B 253 O PHE B 270 SHEET 5 D 7 ARG B 156 TYR B 163 -1 N MET B 160 O ILE B 254 SHEET 6 D 7 HIS B 214 PRO B 219 -1 O VAL B 218 N VAL B 157 SHEET 7 D 7 GLU B 204 ASP B 207 -1 N LEU B 206 O SER B 215 SHEET 1 E 4 ARG D 110 GLY D 112 0 SHEET 2 E 4 CYS D 141 TRP D 146 -1 O TRP D 146 N ARG D 110 SHEET 3 E 4 THR D 230 TYR D 236 -1 O THR D 230 N LEU D 145 SHEET 4 E 4 ILE D 195 VAL D 197 -1 N ARG D 196 O ASN D 235 SHEET 1 F 7 CYS D 124 SER D 127 0 SHEET 2 F 7 LYS D 132 CYS D 135 -1 O PHE D 134 N THR D 125 SHEET 3 F 7 LEU D 264 VAL D 274 1 O GLU D 271 N MET D 133 SHEET 4 F 7 ILE D 251 GLU D 258 -1 N THR D 253 O PHE D 270 SHEET 5 F 7 ARG D 156 TYR D 163 -1 N MET D 160 O ILE D 254 SHEET 6 F 7 HIS D 214 PRO D 219 -1 O VAL D 218 N VAL D 157 SHEET 7 F 7 GLU D 204 ASP D 207 -1 N LEU D 206 O SER D 215 SHEET 1 G 4 ARG C 110 GLY C 112 0 SHEET 2 G 4 CYS C 141 TRP C 146 -1 O TRP C 146 N ARG C 110 SHEET 3 G 4 THR C 230 TYR C 236 -1 O THR C 230 N LEU C 145 SHEET 4 G 4 ILE C 195 VAL C 197 -1 N ARG C 196 O ASN C 235 SHEET 1 H 7 CYS C 124 SER C 127 0 SHEET 2 H 7 LYS C 132 CYS C 135 -1 O PHE C 134 N THR C 125 SHEET 3 H 7 ASN C 263 VAL C 274 1 O GLU C 271 N MET C 133 SHEET 4 H 7 ILE C 251 ASP C 259 -1 N THR C 253 O PHE C 270 SHEET 5 H 7 THR C 155 TYR C 163 -1 N MET C 160 O ILE C 254 SHEET 6 H 7 HIS C 214 PRO C 219 -1 O VAL C 218 N VAL C 157 SHEET 7 H 7 GLU C 204 ASP C 207 -1 N LEU C 206 O SER C 215 LINK ZN ZN A 1 SG CYS A 176 1555 1555 2.41 LINK ZN ZN A 1 ND1 HIS A 179 1555 1555 2.04 LINK ZN ZN A 1 SG CYS A 238 1555 1555 2.47 LINK ZN ZN A 1 SG CYS A 242 1555 1555 2.30 LINK ZN ZN B 1 SG CYS B 176 1555 1555 2.35 LINK ZN ZN B 1 ND1 HIS B 179 1555 1555 2.12 LINK ZN ZN B 1 SG CYS B 238 1555 1555 2.34 LINK ZN ZN B 1 SG CYS B 242 1555 1555 2.28 LINK ZN ZN D 1 SG CYS D 176 1555 1555 2.34 LINK ZN ZN D 1 ND1 HIS D 179 1555 1555 2.19 LINK ZN ZN D 1 SG CYS D 238 1555 1555 2.43 LINK ZN ZN D 1 SG CYS D 242 1555 1555 2.35 LINK ZN ZN C 1 SG CYS C 176 1555 1555 2.42 LINK ZN ZN C 1 ND1 HIS C 179 1555 1555 2.03 LINK ZN ZN C 1 SG CYS C 238 1555 1555 2.39 LINK ZN ZN C 1 SG CYS C 242 1555 1555 2.24 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 4 CYS D 176 HIS D 179 CYS D 238 CYS D 242 SITE 1 AC4 4 CYS C 176 HIS C 179 CYS C 238 CYS C 242 CRYST1 65.084 93.713 145.570 90.00 90.00 90.00 P 21 21 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006870 0.00000