HEADER TRANSCRIPTION 06-JUL-20 6ZNC TITLE STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY A SMALL TITLE 2 MOLECULE: METHYLENE QUINUCLIDINONE (MQ). HUMAN WILD-TYPE P53DBD BOUND TITLE 3 TO DNA AND MQ: WT-DNA-MQ (I) 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 MOL_ID: 2; COMPND 8 MOLECULE: DNA TARGET; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: P53 DNA TARGET; COMPND 11 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: 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: INTEGRATED DNA TECHNOLOGIES, ISRAEL 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 H.ROZENBERG,O.DEGTJARIK,Y.DISKIN-POSNER,Z.SHAKKED REVDAT 3 31-JAN-24 6ZNC 1 REMARK REVDAT 2 15-DEC-21 6ZNC 1 JRNL REVDAT 1 08-DEC-21 6ZNC 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. 1.64 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 27440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1933 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 46.6100 - 3.9600 0.99 1907 146 0.1468 0.1797 REMARK 3 2 3.9600 - 3.1400 0.99 1850 138 0.1446 0.1487 REMARK 3 3 3.1400 - 2.7500 0.99 1854 155 0.1756 0.2142 REMARK 3 4 2.7500 - 2.5000 0.99 1847 137 0.1710 0.1867 REMARK 3 5 2.4900 - 2.3200 0.99 1851 134 0.1674 0.1993 REMARK 3 6 2.3200 - 2.1800 0.99 1855 137 0.1570 0.2087 REMARK 3 7 2.1800 - 2.0700 0.97 1790 135 0.1600 0.1947 REMARK 3 8 2.0700 - 1.9800 0.99 1833 143 0.1636 0.2045 REMARK 3 9 1.9800 - 1.9000 0.99 1834 133 0.1627 0.2015 REMARK 3 10 1.9000 - 1.8400 0.99 1843 136 0.1652 0.1942 REMARK 3 11 1.8400 - 1.7800 0.98 1784 153 0.1764 0.2203 REMARK 3 12 1.7800 - 1.7300 0.97 1833 118 0.1818 0.2558 REMARK 3 13 1.7300 - 1.6800 0.97 1766 140 0.1987 0.2506 REMARK 3 14 1.6800 - 1.6400 0.89 1660 128 0.2101 0.2488 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) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.335 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.54 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 : 0.011 2008 REMARK 3 ANGLE : 1.226 2816 REMARK 3 CHIRALITY : 0.082 310 REMARK 3 PLANARITY : 0.009 328 REMARK 3 DIHEDRAL : 22.878 792 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 167.8759 -13.7802 53.7655 REMARK 3 T TENSOR REMARK 3 T11: 0.2016 T22: 0.2131 REMARK 3 T33: 0.3992 T12: 0.0376 REMARK 3 T13: -0.0591 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 0.3372 L22: 0.8773 REMARK 3 L33: 0.5074 L12: 0.1272 REMARK 3 L13: -0.1343 L23: 0.5435 REMARK 3 S TENSOR REMARK 3 S11: -0.2698 S12: -0.1378 S13: 0.3194 REMARK 3 S21: 0.2442 S22: 0.1568 S23: -0.4842 REMARK 3 S31: 0.0392 S32: 0.0126 S33: -0.0394 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 163 ) REMARK 3 ORIGIN FOR THE GROUP (A): 159.6219 -9.5150 43.8877 REMARK 3 T TENSOR REMARK 3 T11: 0.1549 T22: 0.1782 REMARK 3 T33: 0.2116 T12: 0.0156 REMARK 3 T13: -0.0105 T23: 0.0501 REMARK 3 L TENSOR REMARK 3 L11: 1.2912 L22: 1.2816 REMARK 3 L33: 0.2297 L12: -0.4172 REMARK 3 L13: -0.3677 L23: 0.4671 REMARK 3 S TENSOR REMARK 3 S11: -0.0114 S12: 0.2378 S13: 0.2789 REMARK 3 S21: -0.1313 S22: -0.1461 S23: -0.3106 REMARK 3 S31: -0.0611 S32: 0.0463 S33: -0.0934 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 164 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 148.8723 -15.1098 58.5179 REMARK 3 T TENSOR REMARK 3 T11: 0.1494 T22: 0.1795 REMARK 3 T33: 0.0588 T12: 0.0578 REMARK 3 T13: 0.0096 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.7993 L22: 1.9214 REMARK 3 L33: 2.1051 L12: 0.3934 REMARK 3 L13: 1.0605 L23: 1.4247 REMARK 3 S TENSOR REMARK 3 S11: -0.3653 S12: -0.2158 S13: 0.0335 REMARK 3 S21: 0.1714 S22: 0.1164 S23: 0.2201 REMARK 3 S31: -0.0169 S32: -0.0754 S33: -1.1910 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 142.7939 -22.2493 46.6434 REMARK 3 T TENSOR REMARK 3 T11: 0.2109 T22: 0.2332 REMARK 3 T33: 0.2892 T12: -0.0268 REMARK 3 T13: 0.0081 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 0.1154 L22: 0.1636 REMARK 3 L33: 0.3641 L12: -0.1287 REMARK 3 L13: 0.1974 L23: -0.2364 REMARK 3 S TENSOR REMARK 3 S11: -0.1287 S12: 0.1308 S13: -0.5794 REMARK 3 S21: -0.0427 S22: 0.0642 S23: 0.2910 REMARK 3 S31: -0.0094 S32: -0.3852 S33: 0.0061 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 155.3661 -25.1222 47.3128 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.1495 REMARK 3 T33: 0.0836 T12: 0.0434 REMARK 3 T13: 0.0169 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.7767 L22: 0.2559 REMARK 3 L33: 1.5595 L12: -0.0202 REMARK 3 L13: 0.2148 L23: 0.5971 REMARK 3 S TENSOR REMARK 3 S11: 0.0911 S12: 0.0396 S13: -0.2828 REMARK 3 S21: 0.0685 S22: -0.0283 S23: 0.1394 REMARK 3 S31: 0.3155 S32: -0.0460 S33: 0.6899 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): 158.3995 -15.4766 45.6154 REMARK 3 T TENSOR REMARK 3 T11: 0.1244 T22: 0.1321 REMARK 3 T33: 0.1160 T12: 0.0101 REMARK 3 T13: 0.0142 T23: 0.0389 REMARK 3 L TENSOR REMARK 3 L11: 0.5498 L22: 1.5171 REMARK 3 L33: 0.6428 L12: 0.1237 REMARK 3 L13: 0.5934 L23: -0.1299 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.1803 S13: 0.1105 REMARK 3 S21: -0.0798 S22: -0.0470 S23: -0.1695 REMARK 3 S31: 0.0291 S32: 0.0407 S33: -0.0164 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 264 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 154.3575 -1.2744 49.6983 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.1167 REMARK 3 T33: 0.2486 T12: 0.0167 REMARK 3 T13: -0.0306 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.2282 L22: 0.3052 REMARK 3 L33: 0.3785 L12: 0.2375 REMARK 3 L13: -0.1000 L23: 0.0557 REMARK 3 S TENSOR REMARK 3 S11: 0.0076 S12: 0.0556 S13: 0.2712 REMARK 3 S21: -0.0290 S22: -0.0303 S23: -0.1987 REMARK 3 S31: -0.0887 S32: 0.0014 S33: 0.0371 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 137.4564 2.7442 49.2450 REMARK 3 T TENSOR REMARK 3 T11: 0.3135 T22: 0.3967 REMARK 3 T33: 0.2178 T12: -0.0256 REMARK 3 T13: 0.0019 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 0.6970 L22: 0.5300 REMARK 3 L33: 0.5004 L12: 0.1886 REMARK 3 L13: -0.4440 L23: 0.2377 REMARK 3 S TENSOR REMARK 3 S11: 0.0998 S12: 0.2802 S13: -0.0938 REMARK 3 S21: -0.2947 S22: -0.0508 S23: -0.0708 REMARK 3 S31: -0.2301 S32: 0.3863 S33: 0.0121 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 6ZNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27447 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51500 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 (%): 44.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN/DNA RATIO 1:2.4, TRIS PH=8.5 REMARK 280 100MM, 2.0% TACSIMATE(TM) PH=8.0, 16% W/V PEG 3350, EVAPORATION, REMARK 280 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 68.87200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.76850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.87200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.76850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 270.50990 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 102.07669 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 HOH B 116 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 SER A 183 REMARK 465 ASP A 184 REMARK 465 SER A 185 REMARK 465 ASP A 186 REMARK 465 GLY A 187 REMARK 465 GLY A 226 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 GLN A 104 CG CD OE1 NE2 REMARK 470 LEU A 114 CG CD1 CD2 REMARK 470 HIS A 115 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 118 OG1 CG2 REMARK 470 CYS A 182 CB SG REMARK 470 LEU A 188 CG CD1 CD2 REMARK 470 ARG A 202 NE CZ NH1 NH2 REMARK 470 GLU A 204 CD OE1 OE2 REMARK 470 ASP A 207 OD1 OD2 REMARK 470 GLU A 221 CD OE1 OE2 REMARK 470 VAL A 225 CG1 CG2 REMARK 470 SER A 227 OG REMARK 470 ASP A 228 CG OD1 OD2 REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 ARG A 290 CD NE CZ NH1 NH2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 LYS A 292 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS A 120 O HOH A 401 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 9 O3' DC B 9 C3' -0.067 REMARK 500 REMARK 500 REMARK: NULL 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 DG B 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA B 6 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 TWO ENANTIOMERS, QNN AND QN8 ARE PRODUCED BY REACTION OF THE REMARK 600 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 102.4 REMARK 620 3 CYS A 238 SG 109.8 112.2 REMARK 620 4 CYS A 242 SG 113.4 105.3 113.1 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QNN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QNN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QN8 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QNN A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7B46 RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B47 RELATED DB: PDB REMARK 900 RELATED ID: 7B48 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: 7B4C RELATED DB: PDB REMARK 900 RELATED ID: 7B4D RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4E 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: 7B4H RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4N RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX DBREF 6ZNC A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 6ZNC B 1 12 PDB 6ZNC 6ZNC 1 12 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 ARG ARG THR GLU GLU GLU ASN SEQRES 16 A 200 LEU ARG LYS LYS GLY SEQRES 1 B 12 DC DG DG DG DC DA DT DG DC DC DC DG HET ZN A 301 1 HET QNN A 302 10 HET QNN A 303 10 HET QN8 A 304 10 HET QNN A 305 10 HETNAM ZN ZINC ION HETNAM QNN (2~{S})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE HETNAM QN8 (2~{R})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE FORMUL 3 ZN ZN 2+ FORMUL 4 QNN 3(C8 H13 N O) FORMUL 6 QN8 C8 H13 N O FORMUL 8 HOH *177(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 THR A 140 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 LYS A 132 N SER A 127 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 THR A 253 O PHE A 270 SHEET 5 AA2 7 ARG A 156 TYR A 163 -1 N MET A 160 O ILE A 254 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 GLU A 204 O VAL A 217 LINK SG CYS A 124 C1 AQNN A 302 1555 1555 1.82 LINK SG BCYS A 229 C1 BQNN A 303 1555 1555 1.80 LINK SG CCYS A 229 C1 CQN8 A 304 1555 1555 1.80 LINK SG CYS A 277 C1 AQNN A 305 1555 1555 1.74 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.32 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.03 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 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 SITE 1 AC2 7 LEU A 114 SER A 116 THR A 123 CYS A 124 SITE 2 AC2 7 PRO A 142 SER A 166 DG B 12 SITE 1 AC3 5 TRP A 146 SER A 227 CYS A 229 QN8 A 304 SITE 2 AC3 5 HOH A 450 SITE 1 AC4 3 CYS A 229 QNN A 303 HOH A 450 SITE 1 AC5 4 LYS A 120 SER A 121 ALA A 276 CYS A 277 CRYST1 137.744 49.537 34.066 90.00 92.79 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 0.007260 0.000000 0.000354 0.00000 SCALE2 0.000000 0.020187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029390 0.00000