HEADER PEPTIDE BINDING PROTEIN 13-JAN-21 7DVD TITLE THE CRYSTAL STRUCTURE OF P53 DNA BINDING DOMAIN AND PUMA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ZN; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BCL-2-BINDING COMPONENT 3, ISOFORMS 1/2; COMPND 9 CHAIN: E; COMPND 10 SYNONYM: JFY-1,P53 UP-REGULATED MODULATOR OF APOPTOSIS; 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_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS P53 PUMA BH3 PEPTIDE COMPLEX, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.W.HAN,H.N.LEE,M.S.JEONG,S.B.JANG REVDAT 2 29-NOV-23 7DVD 1 REMARK REVDAT 1 04-AUG-21 7DVD 0 JRNL AUTH C.W.HAN,H.N.LEE,M.S.JEONG,S.Y.PARK,S.B.JANG JRNL TITL STRUCTURAL BASIS OF THE P53 DNA BINDING DOMAIN AND PUMA JRNL TITL 2 COMPLEX. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 548 39 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33631672 JRNL DOI 10.1016/J.BBRC.2021.02.049 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.Y.PARK,S.B.JANG REMARK 1 TITL IN VITRO BINDING PROPERTIES OF TUMOR SUPPRESSOR P53 WITH REMARK 1 TITL 2 PUMA AND NOXA REMARK 1 REF BIOCHEM BIOPHYS RES COMMUN. V.0(2) 350 2012 REMARK 1 REFN ISSN 0006-291X REMARK 1 PMID 22446329 REMARK 1 DOI 10.1016/J.BBRC.2012.03.001 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 50783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.430 REMARK 3 FREE R VALUE TEST SET COUNT : 2756 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6319 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.84 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.385 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : COOT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62203 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5060 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32300 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: NULL REMARK 200 STARTING MODEL: 2WXR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS (PH 7.0) 20% (W/W) PEG-200 REMARK 280 MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 REMARK 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 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 HIS A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS B 291 REMARK 465 HIS B 292 REMARK 465 HIS B 293 REMARK 465 HIS B 294 REMARK 465 HIS B 295 REMARK 465 HIS B 296 REMARK 465 HIS C 291 REMARK 465 HIS C 292 REMARK 465 HIS C 293 REMARK 465 HIS C 294 REMARK 465 HIS C 295 REMARK 465 HIS C 296 REMARK 465 HIS D 291 REMARK 465 HIS D 292 REMARK 465 HIS D 293 REMARK 465 HIS D 294 REMARK 465 HIS D 295 REMARK 465 HIS D 296 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 LYS A 101 CE NZ REMARK 470 LYS A 120 CE NZ REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 101 CE NZ REMARK 470 LYS B 120 CE NZ REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 101 CE NZ REMARK 470 LYS C 120 CE NZ REMARK 470 ARG C 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 101 CE NZ REMARK 470 LYS D 120 CE NZ REMARK 470 ARG D 209 CG CD NE CZ NH1 NH2 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 OD1 ASP D 186 O HOH D 401 2.10 REMARK 500 OE2 GLU A 204 O HOH A 401 2.12 REMARK 500 O SER B 116 O HOH B 401 2.12 REMARK 500 NH2 ARG A 175 OD2 ASP A 184 2.14 REMARK 500 O VAL D 147 O HOH D 402 2.16 REMARK 500 NH2 ARG C 202 OE2 GLU C 221 2.17 REMARK 500 NE2 GLN C 136 O HOH C 401 2.19 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 CYS D 135 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 LEU E 17 CA - CB - CG ANGL. DEV. = 20.2 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 CYS A 275 -168.63 -123.87 REMARK 500 ASN A 288 -82.53 -25.79 REMARK 500 SER B 95 7.00 -48.38 REMARK 500 TYR B 103 109.07 -162.01 REMARK 500 LEU B 137 132.14 -38.49 REMARK 500 ALA B 138 8.79 58.17 REMARK 500 GLN B 167 1.64 -69.27 REMARK 500 SER B 183 38.74 -91.38 REMARK 500 ASN B 210 -71.16 -105.84 REMARK 500 GLU B 224 174.44 -58.26 REMARK 500 LEU B 289 79.69 -69.92 REMARK 500 PHE C 212 -3.16 78.95 REMARK 500 LEU D 137 121.21 -39.35 REMARK 500 ALA D 138 16.14 52.99 REMARK 500 ASP D 186 35.61 -63.15 REMARK 500 ASN D 288 -169.67 -53.24 REMARK 500 LEU D 289 -15.93 83.42 REMARK 500 ILE E 6 -158.12 -146.76 REMARK 500 LEU E 10 36.41 -77.54 REMARK 500 LEU E 17 -30.67 -32.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU E 10 ARG E 11 148.90 REMARK 500 ARG E 11 ARG E 12 148.33 REMARK 500 ASP E 16 LEU E 17 133.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 421 DISTANCE = 8.66 ANGSTROMS REMARK 525 HOH A 422 DISTANCE = 8.71 ANGSTROMS REMARK 525 HOH E 111 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH E 112 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH E 113 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH E 114 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH E 115 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH E 116 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH E 117 DISTANCE = 7.79 ANGSTROMS REMARK 525 HOH E 118 DISTANCE = 8.87 ANGSTROMS REMARK 525 HOH E 119 DISTANCE = 9.30 ANGSTROMS 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 103.1 REMARK 620 3 CYS A 238 SG 112.6 110.6 REMARK 620 4 CYS A 242 SG 120.7 104.7 104.7 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 95.1 108.5 REMARK 620 4 CYS B 242 SG 117.1 123.9 106.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 176 SG REMARK 620 2 HIS C 179 ND1 89.1 REMARK 620 3 CYS C 238 SG 115.2 102.1 REMARK 620 4 CYS C 242 SG 134.2 98.8 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 176 SG REMARK 620 2 HIS D 179 ND1 83.8 REMARK 620 3 CYS D 242 SG 137.0 108.9 REMARK 620 N 1 2 DBREF 7DVD A 92 290 UNP P04637 P53_HUMAN 92 290 DBREF 7DVD B 92 290 UNP P04637 P53_HUMAN 92 290 DBREF 7DVD C 92 290 UNP P04637 P53_HUMAN 92 290 DBREF 7DVD D 92 290 UNP P04637 P53_HUMAN 92 290 DBREF 7DVD E 5 19 UNP Q9BXH1 BBC3_HUMAN 136 150 SEQADV 7DVD HIS A 291 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS A 292 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS A 293 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS A 294 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS A 295 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS A 296 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 291 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 292 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 293 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 294 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 295 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS B 296 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 291 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 292 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 293 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 294 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 295 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS C 296 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 291 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 292 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 293 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 294 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 295 UNP P04637 EXPRESSION TAG SEQADV 7DVD HIS D 296 UNP P04637 EXPRESSION TAG SEQRES 1 A 205 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 A 205 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 A 205 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 A 205 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 A 205 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 A 205 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 A 205 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 A 205 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 A 205 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 A 205 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 A 205 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 A 205 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 A 205 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 A 205 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 A 205 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 A 205 GLU ASN LEU ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 205 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 B 205 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 B 205 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 B 205 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 B 205 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 B 205 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 B 205 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 B 205 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 B 205 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 B 205 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 B 205 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 B 205 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 B 205 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 B 205 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 B 205 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 B 205 GLU ASN LEU ARG HIS HIS HIS HIS HIS HIS SEQRES 1 C 205 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 C 205 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 C 205 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 C 205 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 C 205 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 C 205 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 C 205 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 C 205 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 C 205 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 C 205 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 C 205 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 C 205 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 C 205 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 C 205 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 C 205 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 C 205 GLU ASN LEU ARG HIS HIS HIS HIS HIS HIS SEQRES 1 D 205 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 2 D 205 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 3 D 205 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 4 D 205 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 5 D 205 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 6 D 205 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 7 D 205 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 8 D 205 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 9 D 205 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 10 D 205 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 11 D 205 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 12 D 205 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 13 D 205 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 14 D 205 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 15 D 205 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 16 D 205 GLU ASN LEU ARG HIS HIS HIS HIS HIS HIS SEQRES 1 E 15 GLU ILE GLY ALA GLN LEU ARG ARG MET ALA ASP ASP LEU SEQRES 2 E 15 ASN ALA HET ZN A 301 1 HET ZN B 301 1 HET ZN C 301 1 HET ZN D 301 1 HETNAM ZN ZINC ION FORMUL 6 ZN 4(ZN 2+) FORMUL 10 HOH *89(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 LEU A 289 1 13 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 LEU B 289 1 13 HELIX 7 AA7 GLN C 165 MET C 169 5 5 HELIX 8 AA8 CYS C 176 ARG C 181 1 6 HELIX 9 AA9 CYS C 277 LEU C 289 1 13 HELIX 10 AB1 GLN D 165 MET D 169 5 5 HELIX 11 AB2 CYS D 176 CYS D 182 1 7 HELIX 12 AB3 CYS D 277 ASN D 288 1 12 HELIX 13 AB4 ALA E 8 ARG E 12 5 5 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 GLN A 136 -1 O PHE A 134 N THR A 125 SHEET 3 AA2 7 LEU A 264 CYS A 275 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 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 SHEET 1 AA3 4 ARG B 110 GLY B 112 0 SHEET 2 AA3 4 CYS B 141 TRP B 146 -1 O GLN B 144 N GLY B 112 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 VAL B 197 -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 GLN B 136 -1 O LYS B 132 N SER B 127 SHEET 3 AA4 7 LEU B 264 CYS B 275 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 MET B 160 O ILE B 254 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 LEU B 206 O SER B 215 SHEET 1 AA5 4 ARG C 110 GLY C 112 0 SHEET 2 AA5 4 CYS C 141 TRP C 146 -1 O TRP C 146 N ARG C 110 SHEET 3 AA5 4 THR C 230 TYR C 236 -1 O TYR C 234 N CYS C 141 SHEET 4 AA5 4 ILE C 195 GLU C 198 -1 N GLU C 198 O HIS C 233 SHEET 1 AA6 7 CYS C 124 SER C 127 0 SHEET 2 AA6 7 LYS C 132 CYS C 135 -1 O PHE C 134 N THR C 125 SHEET 3 AA6 7 LEU C 264 VAL C 274 1 O GLU C 271 N MET C 133 SHEET 4 AA6 7 ILE C 251 GLU C 258 -1 N LEU C 257 O LEU C 265 SHEET 5 AA6 7 ARG C 156 TYR C 163 -1 N MET C 160 O ILE C 254 SHEET 6 AA6 7 HIS C 214 PRO C 219 -1 O VAL C 218 N VAL C 157 SHEET 7 AA6 7 GLU C 204 ASP C 207 -1 N GLU C 204 O VAL C 217 SHEET 1 AA7 4 ARG D 110 GLY D 112 0 SHEET 2 AA7 4 CYS D 141 TRP D 146 -1 O GLN D 144 N GLY D 112 SHEET 3 AA7 4 THR D 230 TYR D 236 -1 O TYR D 234 N CYS D 141 SHEET 4 AA7 4 ILE D 195 VAL D 197 -1 N ARG D 196 O ASN D 235 SHEET 1 AA8 7 CYS D 124 SER D 127 0 SHEET 2 AA8 7 LYS D 132 CYS D 135 -1 O LYS D 132 N SER D 127 SHEET 3 AA8 7 LEU D 264 VAL D 274 1 O GLU D 271 N MET D 133 SHEET 4 AA8 7 ILE D 251 GLU D 258 -1 N LEU D 257 O LEU D 265 SHEET 5 AA8 7 ARG D 156 TYR D 163 -1 N MET D 160 O ILE D 254 SHEET 6 AA8 7 HIS D 214 PRO D 219 -1 O VAL D 218 N VAL D 157 SHEET 7 AA8 7 GLU D 204 ASP D 207 -1 N LEU D 206 O SER D 215 SSBOND 1 CYS C 135 CYS C 141 1555 1555 2.07 SSBOND 2 CYS D 135 CYS D 141 1555 1555 2.08 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.45 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.30 LINK SG CYS A 238 ZN ZN A 301 1555 1555 1.95 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.71 LINK SG CYS B 176 ZN ZN B 301 1555 1555 2.94 LINK ND1 HIS B 179 ZN ZN B 301 1555 1555 2.20 LINK SG CYS B 238 ZN ZN B 301 1555 1555 2.25 LINK SG CYS B 242 ZN ZN B 301 1555 1555 2.38 LINK SG CYS C 176 ZN ZN C 301 1555 1555 2.32 LINK ND1 HIS C 179 ZN ZN C 301 1555 1555 2.55 LINK SG CYS C 238 ZN ZN C 301 1555 1555 2.16 LINK SG CYS C 242 ZN ZN C 301 1555 1555 2.17 LINK SG CYS D 176 ZN ZN D 301 1555 1555 2.30 LINK ND1 HIS D 179 ZN ZN D 301 1555 1555 2.48 LINK SG CYS D 242 ZN ZN D 301 1555 1555 2.44 CRYST1 68.612 73.411 84.408 89.94 89.82 90.00 P 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 0.014575 -0.000001 -0.000045 0.00000 SCALE2 0.000000 0.013622 -0.000014 0.00000 SCALE3 0.000000 0.000000 0.011847 0.00000