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 4 13-NOV-24 6ZNC 1 REMARK
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 <I/SIGMA(I)> 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 <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: 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