HEADER TRANSCRIPTION 02-DEC-20 7B49 TITLE STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY A SMALL TITLE 2 MOLECULE: METHYLENE QUINUCLIDINONE (MQ). HUMAN P53DBD-R273H MUTANT TITLE 3 BOUND TO DNA AND MQ: R273H-DNA-MQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B; 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: C; 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 H.ROZENBERG,O.DEGTJARIK,Z.SHAKKED REVDAT 3 31-JAN-24 7B49 1 REMARK REVDAT 2 15-DEC-21 7B49 1 JRNL REVDAT 1 08-DEC-21 7B49 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 85297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4265 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 34.1100 - 4.4100 0.94 2697 138 0.1695 0.2225 REMARK 3 2 4.4100 - 3.5000 0.99 2790 140 0.1279 0.1669 REMARK 3 3 3.5000 - 3.0600 0.99 2781 145 0.1400 0.1810 REMARK 3 4 3.0600 - 2.7800 1.00 2743 145 0.1590 0.1865 REMARK 3 5 2.7800 - 2.5800 0.96 2675 155 0.1597 0.2006 REMARK 3 6 2.5800 - 2.4300 0.97 2674 134 0.1692 0.1889 REMARK 3 7 2.4300 - 2.3100 0.97 2712 132 0.1684 0.2243 REMARK 3 8 2.3100 - 2.2100 0.99 2698 155 0.1649 0.2035 REMARK 3 9 2.2100 - 2.1200 0.99 2750 141 0.1653 0.2116 REMARK 3 10 2.1200 - 2.0500 0.99 2752 137 0.1635 0.2340 REMARK 3 11 2.0500 - 1.9800 0.99 2718 154 0.1622 0.2416 REMARK 3 12 1.9800 - 1.9300 0.99 2712 136 0.1614 0.2236 REMARK 3 13 1.9300 - 1.8800 0.99 2749 143 0.1768 0.2246 REMARK 3 14 1.8800 - 1.8300 0.95 2624 136 0.1798 0.2157 REMARK 3 15 1.8300 - 1.7900 0.97 2663 150 0.1945 0.2505 REMARK 3 16 1.7900 - 1.7500 0.98 2715 143 0.1848 0.2223 REMARK 3 17 1.7500 - 1.7200 0.98 2685 138 0.1962 0.2707 REMARK 3 18 1.7200 - 1.6800 0.98 2677 143 0.2140 0.2341 REMARK 3 19 1.6800 - 1.6500 0.98 2674 146 0.2135 0.2588 REMARK 3 20 1.6500 - 1.6300 0.99 2725 138 0.2258 0.3170 REMARK 3 21 1.6300 - 1.6000 0.99 2713 150 0.2333 0.2672 REMARK 3 22 1.6000 - 1.5700 0.99 2712 130 0.2384 0.3239 REMARK 3 23 1.5700 - 1.5500 0.99 2693 143 0.2489 0.3085 REMARK 3 24 1.5500 - 1.5300 0.99 2741 156 0.2521 0.3076 REMARK 3 25 1.5300 - 1.5100 0.99 2689 134 0.2623 0.3156 REMARK 3 26 1.5100 - 1.4900 0.96 2628 139 0.2872 0.3339 REMARK 3 27 1.4900 - 1.4700 0.96 2629 133 0.2843 0.2963 REMARK 3 28 1.4700 - 1.4500 0.97 2668 137 0.2991 0.3617 REMARK 3 29 1.4500 - 1.4400 0.97 2666 149 0.3157 0.3631 REMARK 3 30 1.4400 - 1.4200 0.98 2679 145 0.3205 0.3147 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.712 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.79 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 : 0.008 4066 REMARK 3 ANGLE : 1.043 5640 REMARK 3 CHIRALITY : 0.080 606 REMARK 3 PLANARITY : 0.006 660 REMARK 3 DIHEDRAL : 21.120 1572 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 7B49 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_1292111695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-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 : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97200 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 : 93002 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 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: 4IBS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN/DNA RATIO 1:1.4, 0.075M SODIUM REMARK 280 FORMATE, 7.5% 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 68.34250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.02800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.34250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.02800 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, C 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 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -4.23953 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 68.22140 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 C 242 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 116 REMARK 465 GLY A 117 REMARK 465 THR A 118 REMARK 465 SER A 183 REMARK 465 ASP A 184 REMARK 465 SER B 116 REMARK 465 GLY B 117 REMARK 465 THR B 118 REMARK 465 SER B 183 REMARK 465 ASP B 184 REMARK 465 DT C 1 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 HIS A 115 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 121 CB OG REMARK 470 LEU A 188 CG CD1 CD2 REMARK 470 ARG A 202 NE CZ NH1 NH2 REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 287 CD OE1 OE2 REMARK 470 ARG A 290 CD NE CZ NH1 NH2 REMARK 470 LYS A 291 CE NZ REMARK 470 LYS A 292 CE NZ REMARK 470 HIS B 115 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 121 CB OG REMARK 470 LEU B 188 CG CD1 CD2 REMARK 470 ARG B 202 NE CZ NH1 NH2 REMARK 470 ARG B 283 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 287 CD OE1 OE2 REMARK 470 ARG B 290 CD NE CZ NH1 NH2 REMARK 470 LYS B 291 CE NZ REMARK 470 LYS B 292 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 OG SER B 96 O HOH B 401 2.12 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 DT C 7 O3' DT C 7 C3' -0.054 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 C 8 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 DG C 8 O5' - P - OP1 ANGL. DEV. = -8.2 DEGREES REMARK 500 DG C 18 OP1 - P - OP2 ANGL. DEV. = 10.4 DEGREES REMARK 500 DG C 18 O5' - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 104.0 REMARK 620 3 CYS A 238 SG 111.4 110.9 REMARK 620 4 CYS A 242 SG 113.9 104.4 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 176 SG REMARK 620 2 HIS B 179 ND1 101.7 REMARK 620 3 CYS B 238 SG 107.7 113.0 REMARK 620 4 CYS B 242 SG 117.0 102.2 114.4 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: 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: 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: 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 7B49 A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 7B49 B 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 7B49 C 1 21 PDB 7B49 7B49 1 21 SEQADV 7B49 HIS A 273 UNP P04637 ARG 273 ENGINEERED MUTATION SEQADV 7B49 HIS B 273 UNP P04637 ARG 273 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 HIS 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 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 B 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 B 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 B 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 B 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 B 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 B 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 B 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 B 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 B 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 B 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 B 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 B 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 B 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL HIS VAL CYS SEQRES 15 B 200 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 B 200 LEU ARG LYS LYS GLY SEQRES 1 C 21 DT DG DG DG DC DA DT DG DC DC DC DG DG SEQRES 2 C 21 DG DC DA DT DG DC DC DC HET ZN A 301 1 HET QN8 A 302 10 HET QNN A 303 10 HET FMT A 304 3 HET FMT A 305 3 HET FMT A 306 3 HET FMT A 307 3 HET FMT A 308 3 HET FMT A 309 3 HET FMT A 310 3 HET FMT A 311 3 HET FMT A 312 3 HET ACT A 313 4 HET EDO A 314 4 HET EDO A 315 4 HET EDO A 316 4 HET ZN B 301 1 HET QN8 B 302 10 HET QNN B 303 10 HET FMT B 304 3 HET FMT B 305 3 HET FMT B 306 3 HET FMT B 307 3 HET FMT B 308 3 HET FMT B 309 3 HET FMT B 310 3 HET FMT B 311 3 HET FMT B 312 3 HET FMT B 313 3 HET ACT B 314 4 HET EDO B 315 4 HET FMT C 101 3 HET FMT C 102 3 HET FMT C 103 3 HET FMT C 104 3 HET FMT C 105 3 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 FMT FORMIC ACID HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ZN 2(ZN 2+) FORMUL 5 QN8 2(C8 H13 N O) FORMUL 6 QNN 2(C8 H13 N O) FORMUL 7 FMT 24(C H2 O2) FORMUL 16 ACT 2(C2 H3 O2 1-) FORMUL 17 EDO 4(C2 H6 O2) FORMUL 40 HOH *498(H2 O) HELIX 1 AA1 GLN A 165 MET A 169 5 5 HELIX 2 AA2 CYS A 176 ARG A 181 1 6 HELIX 3 AA3 CYS A 277 GLY A 293 1 17 HELIX 4 AA4 GLN B 165 MET B 169 5 5 HELIX 5 AA5 CYS B 176 ARG B 181 1 6 HELIX 6 AA6 CYS B 277 GLY B 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 GLN A 144 N GLY A 112 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 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 GLU A 204 O VAL A 217 SHEET 1 AA3 4 ARG B 110 GLY B 112 0 SHEET 2 AA3 4 CYS B 141 TRP B 146 -1 O TRP B 146 N ARG B 110 SHEET 3 AA3 4 THR B 230 TYR B 236 -1 O THR B 230 N LEU B 145 SHEET 4 AA3 4 ILE B 195 GLU B 198 -1 N ARG B 196 O ASN B 235 SHEET 1 AA4 7 CYS B 124 SER B 127 0 SHEET 2 AA4 7 LYS B 132 CYS B 135 -1 O LYS B 132 N SER B 127 SHEET 3 AA4 7 LEU B 264 VAL B 274 1 O GLU B 271 N MET B 133 SHEET 4 AA4 7 ILE B 251 GLU B 258 -1 N LEU B 257 O LEU B 265 SHEET 5 AA4 7 ARG B 156 TYR B 163 -1 N ARG B 156 O GLU B 258 SHEET 6 AA4 7 HIS B 214 PRO B 219 -1 O VAL B 218 N VAL B 157 SHEET 7 AA4 7 GLU B 204 ASP B 207 -1 N GLU B 204 O VAL B 217 LINK SG ACYS A 229 C1 AQN8 A 302 1555 1555 1.77 LINK SG ACYS A 277 C1 AQNN A 303 1555 1555 1.77 LINK SG ACYS B 229 C1 AQN8 B 302 1555 1555 1.77 LINK SG ACYS B 277 C1 AQNN B 303 1555 1555 1.77 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.35 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 1.99 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.29 LINK SG CYS B 176 ZN ZN B 301 1555 1555 2.26 LINK ND1 HIS B 179 ZN ZN B 301 1555 1555 2.10 LINK SG CYS B 238 ZN ZN B 301 1555 1555 2.32 LINK SG CYS B 242 ZN ZN B 301 1555 1555 2.35 CRYST1 136.685 50.056 68.353 90.00 93.56 90.00 C 1 2 1 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 0.007316 0.000000 0.000455 0.00000 SCALE2 0.000000 0.019978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014658 0.00000