HEADER TRANSCRIPTION 02-DEC-20 7B4E TITLE STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY A SMALL TITLE 2 MOLECULE: METHYLENE QUINUCLIDINONE (MQ). HUMAN P53DBD-R282W MUTANT TITLE 3 BOUND TO DNA AND MQ: R282W-DNA-MQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P53 HUMAN DNA BINDING DOMAIN; COMPND 5 SYNONYM: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA TARGET; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: P53 DNA TARGET; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TP53, P53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-27-B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: IDT: INTEGRATED DNA TECHNOLOGY KEYWDS P53, TUMOR SUPPRESSOR, DNA BINDING PROTEIN, PROTEIN DNA COMPLEX, KEYWDS 2 MICHAEL ACCEPTOR, MICHAEL REACTION, PROTEIN-DRUG COMPLEX, PROTEIN- KEYWDS 3 DNA-DRUG COMPLEX, LOOP-SHEET-HELIX MOTIF, DNA TARGET, ACTIVATOR, KEYWDS 4 TRANSCRIPTION, HOOGSTEEN BASE-PAIRING EXPDTA X-RAY DIFFRACTION AUTHOR O.DEGTJARIK,H.ROZENBERG,Z.SHAKKED REVDAT 3 31-JAN-24 7B4E 1 REMARK REVDAT 2 15-DEC-21 7B4E 1 JRNL REVDAT 1 08-DEC-21 7B4E 0 JRNL AUTH O.DEGTJARIK,D.GOLOVENKO,Y.DISKIN-POSNER,L.ABRAHMSEN, JRNL AUTH 2 H.ROZENBERG,Z.SHAKKED JRNL TITL STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY JRNL TITL 2 A SMALL MOLECULE: METHYLENE QUINUCLIDINONE (MQ). JRNL REF NAT COMMUN V. 12 7057 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34862374 JRNL DOI 10.1038/S41467-021-27142-6 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 30182 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.660 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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 34.0600 - 3.7900 1.00 2129 156 0.1479 0.1865 REMARK 3 2 3.7900 - 3.0100 1.00 2086 147 0.1441 0.2019 REMARK 3 3 3.0100 - 2.6300 1.00 2080 154 0.1686 0.1962 REMARK 3 4 2.6300 - 2.3900 0.88 1813 130 0.1638 0.1942 REMARK 3 5 2.3900 - 2.2200 0.97 2021 145 0.1687 0.1924 REMARK 3 6 2.2200 - 2.0900 0.98 2023 144 0.1629 0.1849 REMARK 3 7 2.0900 - 1.9800 0.99 2021 146 0.1719 0.1982 REMARK 3 8 1.9800 - 1.9000 0.99 2077 141 0.1719 0.2267 REMARK 3 9 1.9000 - 1.8200 0.98 2023 150 0.1723 0.1927 REMARK 3 10 1.8200 - 1.7600 0.99 2015 141 0.1705 0.2098 REMARK 3 11 1.7600 - 1.7000 0.98 2041 146 0.1848 0.1866 REMARK 3 12 1.7000 - 1.6600 0.98 1987 142 0.2072 0.2258 REMARK 3 13 1.6600 - 1.6100 0.97 2008 147 0.2339 0.2995 REMARK 3 14 1.6100 - 1.5700 0.90 1849 120 0.2905 0.2972 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.192 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 2122 REMARK 3 ANGLE : 1.050 2956 REMARK 3 CHIRALITY : 0.056 319 REMARK 3 PLANARITY : 0.005 346 REMARK 3 DIHEDRAL : 26.506 845 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4839 -9.7689 14.6163 REMARK 3 T TENSOR REMARK 3 T11: 0.1235 T22: 0.1245 REMARK 3 T33: 0.1519 T12: -0.0076 REMARK 3 T13: -0.0212 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 1.0846 L22: 1.0784 REMARK 3 L33: 0.1410 L12: -0.2194 REMARK 3 L13: -0.2443 L23: 0.2291 REMARK 3 S TENSOR REMARK 3 S11: -0.0527 S12: 0.0056 S13: 0.1473 REMARK 3 S21: -0.0261 S22: -0.0006 S23: -0.1025 REMARK 3 S31: -0.0004 S32: 0.0088 S33: 0.0226 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6572 -16.2869 14.8987 REMARK 3 T TENSOR REMARK 3 T11: 0.1195 T22: 0.0845 REMARK 3 T33: 0.1046 T12: 0.0047 REMARK 3 T13: -0.0072 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.3318 L22: 0.8519 REMARK 3 L33: 0.5066 L12: -0.1902 REMARK 3 L13: 0.3217 L23: 0.0596 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: 0.0531 S13: 0.0560 REMARK 3 S21: 0.0299 S22: -0.0261 S23: -0.0359 REMARK 3 S31: -0.0353 S32: -0.0633 S33: 0.0771 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6423 -23.5848 10.9590 REMARK 3 T TENSOR REMARK 3 T11: 0.1159 T22: 0.1439 REMARK 3 T33: 0.1753 T12: -0.0039 REMARK 3 T13: -0.0076 T23: -0.0345 REMARK 3 L TENSOR REMARK 3 L11: 3.7711 L22: 1.7549 REMARK 3 L33: 0.1585 L12: -0.8491 REMARK 3 L13: -0.5486 L23: -0.0843 REMARK 3 S TENSOR REMARK 3 S11: 0.0164 S12: 0.2562 S13: -0.5528 REMARK 3 S21: -0.0772 S22: -0.0736 S23: 0.2332 REMARK 3 S31: 0.1478 S32: -0.2741 S33: 0.0714 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.2144 -26.8407 12.0300 REMARK 3 T TENSOR REMARK 3 T11: 0.1359 T22: 0.1136 REMARK 3 T33: 0.0819 T12: 0.0105 REMARK 3 T13: 0.0046 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.9797 L22: 1.4173 REMARK 3 L33: 1.9025 L12: -0.0225 REMARK 3 L13: 0.0785 L23: -0.0126 REMARK 3 S TENSOR REMARK 3 S11: 0.0843 S12: 0.0918 S13: -0.1397 REMARK 3 S21: -0.0091 S22: 0.0512 S23: 0.0705 REMARK 3 S31: 0.2150 S32: 0.0363 S33: 0.0233 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2739 -15.7768 11.4972 REMARK 3 T TENSOR REMARK 3 T11: 0.1052 T22: 0.1103 REMARK 3 T33: 0.0891 T12: -0.0012 REMARK 3 T13: 0.0063 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.0383 L22: 1.2590 REMARK 3 L33: 0.5718 L12: -0.3068 REMARK 3 L13: 0.3784 L23: -0.0333 REMARK 3 S TENSOR REMARK 3 S11: -0.0305 S12: 0.1285 S13: 0.0877 REMARK 3 S21: -0.0598 S22: -0.0169 S23: -0.0709 REMARK 3 S31: -0.0081 S32: 0.0032 S33: 0.0191 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3793 5.6912 15.1254 REMARK 3 T TENSOR REMARK 3 T11: 0.1688 T22: 0.1682 REMARK 3 T33: 0.2565 T12: 0.0034 REMARK 3 T13: 0.0006 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 2.1459 L22: 2.0573 REMARK 3 L33: 2.8442 L12: 1.6209 REMARK 3 L13: 2.0965 L23: 1.7224 REMARK 3 S TENSOR REMARK 3 S11: -0.1164 S12: 0.0976 S13: 0.3363 REMARK 3 S21: -0.1548 S22: 0.0624 S23: 0.0897 REMARK 3 S31: -0.1757 S32: 0.2285 S33: 0.0149 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8544 2.4652 13.8684 REMARK 3 T TENSOR REMARK 3 T11: 0.2663 T22: 0.2585 REMARK 3 T33: 0.2113 T12: -0.0152 REMARK 3 T13: -0.0181 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.9700 L22: 2.5801 REMARK 3 L33: 3.3537 L12: -0.1394 REMARK 3 L13: -0.2763 L23: 0.1278 REMARK 3 S TENSOR REMARK 3 S11: 0.2201 S12: 0.3195 S13: 0.1304 REMARK 3 S21: -0.3430 S22: 0.0034 S23: 0.1435 REMARK 3 S31: -0.2464 S32: 0.3293 S33: -0.1549 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 7B4E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292111700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30188 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 2AC0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN/DNA RATIO 1:1.5, 0.1M SODIUM REMARK 280 ACETATE, 20% W/V PEG 3350, PH 6.1, EVAPORATION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.25250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.77650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.25250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.77650 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: TETRAMER REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMER REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -2.00591 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.34071 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C5 PG4 A 306 LIES ON A SPECIAL POSITION. 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 LEU A 114 REMARK 465 HIS A 115 REMARK 465 SER A 116 REMARK 465 GLY A 117 REMARK 465 THR A 118 REMARK 465 ALA A 119 REMARK 465 LYS A 120 REMARK 465 SER A 121 REMARK 465 SER A 183 REMARK 465 ASP A 184 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 188 CG CD1 CD2 REMARK 470 GLU A 287 CD OE1 OE2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 LYS A 292 CD CE NZ REMARK 470 DC B 11 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC B 11 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC B 11 C6 REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 TWO ENANTIOMERS, QNN AND QN8 ARE PRODUCED BY ADDITION REACTION OF REMARK 600 THE MICHAEL ACCEPTOR COMPOUND "2-METHYLENEQUINUCLIDIN-3-ONE" WITH REMARK 600 CYSTEINE OR LYSINE. AS SUCH, QNN AND QN8 BIND COVALENTLY TO THE REMARK 600 THIOL GROUP OF CYSTEINE OR AMINO GROUP OF LYSINE. THE CHIRAL REMARK 600 DEFINITIONS OF QNN AND QN8 BOUND TO CYSTEINES ARE REVERSED TO THAT REMARK 600 OF THE PSEUDO FREE LIGANDS. 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 103.4 REMARK 620 3 CYS A 238 SG 109.7 114.5 REMARK 620 4 CYS A 242 SG 114.1 102.6 112.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZNC RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B47 RELATED DB: PDB REMARK 900 RELATED ID: 7B49 RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4A RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4B RELATED DB: PDB REMARK 900 RELATED ID: 7B4D RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4F RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4G RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4N RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4H RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B46 RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B48 RELATED DB: PDB REMARK 900 RELATED ID: 7B4C RELATED DB: PDB DBREF 7B4E A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 7B4E B 1 11 PDB 7B4E 7B4E 1 11 SEQADV 7B4E TRP A 282 UNP P04637 ARG 282 ENGINEERED MUTATION SEQRES 1 A 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 A 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 A 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 A 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 A 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 A 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 A 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 A 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 A 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 A 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 A 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 A 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 A 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 A 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG VAL CYS SEQRES 15 A 200 ALA CYS PRO GLY ARG ASP TRP ARG THR GLU GLU GLU ASN SEQRES 16 A 200 LEU ARG LYS LYS GLY SEQRES 1 B 11 DC DG DG DG DC DA DT DG DC DC DC HET ZN A 301 1 HET QN8 A 302 10 HET QN8 A 303 10 HET QNN A 304 10 HET QN8 A 305 10 HET PG4 A 306 13 HET EDO A 307 8 HET EDO A 308 4 HETNAM ZN ZINC ION HETNAM QN8 (2~{R})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE HETNAM QNN (2~{S})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN ZN 2+ FORMUL 4 QN8 3(C8 H13 N O) FORMUL 6 QNN C8 H13 N O FORMUL 8 PG4 C8 H18 O5 FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 HOH *274(H2 O) HELIX 1 AA1 GLN A 165 MET A 169 5 5 HELIX 2 AA2 CYS A 176 CYS A 182 1 7 HELIX 3 AA3 CYS A 277 GLY A 293 1 17 SHEET 1 AA1 4 ARG A 110 GLY A 112 0 SHEET 2 AA1 4 CYS A 141 TRP A 146 -1 O TRP A 146 N ARG A 110 SHEET 3 AA1 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 AA1 4 ILE A 195 GLU A 198 -1 N ARG A 196 O ASN A 235 SHEET 1 AA2 7 CYS A 124 SER A 127 0 SHEET 2 AA2 7 LYS A 132 CYS A 135 -1 O PHE A 134 N THR A 125 SHEET 3 AA2 7 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 4 AA2 7 ILE A 251 GLU A 258 -1 N LEU A 257 O LEU A 265 SHEET 5 AA2 7 ARG A 156 TYR A 163 -1 N ARG A 156 O GLU A 258 SHEET 6 AA2 7 HIS A 214 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 7 AA2 7 GLU A 204 ASP A 207 -1 N LEU A 206 O SER A 215 LINK SG ACYS A 124 C1 AQN8 A 302 1555 1555 1.79 LINK SG CYS A 229 C1 AQN8 A 303 1555 1555 1.83 LINK SG BCYS A 277 C1 BQNN A 304 1555 1555 1.79 LINK SG ACYS A 277 C1 AQN8 A 305 1555 1555 1.81 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.31 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.05 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.30 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.34 CRYST1 136.505 49.553 33.401 90.00 93.44 90.00 C 1 2 1 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 0.007326 0.000000 0.000441 0.00000 SCALE2 0.000000 0.020180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029993 0.00000