HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 05-JUN-18 6DMK TITLE A MULTICONFORMER LIGAND MODEL OF AN ISOXAZOLYL-BENZIMIDAZOLE LIGAND TITLE 2 BOUND TO THE BROMODOMAIN OF HUMAN CREBBP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.1.48; COMPND 5 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: CREBBP, CBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, MULTI CONFORMER MODEL, TRANSCRIPTION, TRANSCRIPTION- KEYWDS 2 TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.HUDSON,G.VAN ZUNDERT,D.A.KEEDY,R.FONSECA,A.HELIOU,P.SURESH, AUTHOR 2 K.BORRELLI,T.DAY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 4 01-MAY-24 6DMK 1 AUTHOR REVDAT 3 13-MAR-24 6DMK 1 REMARK REVDAT 2 24-APR-19 6DMK 1 JRNL REVDAT 1 19-DEC-18 6DMK 0 JRNL AUTH G.C.P.VAN ZUNDERT,B.M.HUDSON,S.H.P.DE OLIVEIRA,D.A.KEEDY, JRNL AUTH 2 R.FONSECA,A.HELIOU,P.SURESH,K.BORRELLI,T.DAY,J.S.FRASER, JRNL AUTH 3 H.VAN DEN BEDEM JRNL TITL QFIT-LIGAND REVEALS WIDESPREAD CONFORMATIONAL HETEROGENEITY JRNL TITL 2 OF DRUG-LIKE MOLECULES IN X-RAY ELECTRON DENSITY MAPS. JRNL REF J. MED. CHEM. V. 61 11183 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30457858 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01292 REMARK 0 REMARK 0 THIS ENTRY 6DMK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 4NR5, DETERMINED BY P.FILIPPAKOPOULOS,S.PICAUD, REMARK 0 I.FELLETAR,D.HAY,O.FEDOROV,S.MARTIN,A.W.PIKE,F.VON DELFT, REMARK 0 P.BRENNAN,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP, REMARK 0 STRUCTURAL GENOMICS CONSORTIUM (SGC) REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11_2558 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 13079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 19.2992 - 2.8362 0.95 2489 130 0.1797 0.2032 REMARK 3 2 2.8362 - 2.2523 0.97 2503 128 0.2180 0.2423 REMARK 3 3 2.2523 - 1.9679 0.96 2475 139 0.1992 0.2794 REMARK 3 4 1.9679 - 1.7881 0.97 2473 127 0.2362 0.2996 REMARK 3 5 1.7881 - 1.6600 0.98 2494 121 0.2763 0.3052 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.89 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 : 0.015 1031 REMARK 3 ANGLE : 1.384 1403 REMARK 3 CHIRALITY : 0.061 138 REMARK 3 PLANARITY : 0.011 175 REMARK 3 DIHEDRAL : 15.682 603 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 6DMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13513 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 19.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 4NR5 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20M NANO3, 20.0% PEG 3350, 10.0% REMARK 280 ETGLY, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.15550 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A1083 CG CD CE NZ REMARK 470 ILE A1084 CG1 CG2 CD1 REMARK 470 LYS A1086 CG CD CE NZ REMARK 470 GLU A1088 CD OE1 OE2 REMARK 470 GLU A1089 CG CD OE1 OE2 REMARK 470 GLN A1092 CD OE1 NE2 REMARK 470 ASP A1190 CG OD1 OD2 REMARK 470 GLN A1194 CG CD OE1 NE2 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 HZ2 LYS A 1180 O HOH A 1301 1.37 REMARK 500 OE2 GLU A 1183 O HOH A 1301 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1306 O HOH A 1357 1655 1.96 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 ASP A1190 -70.16 -45.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2LL A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NR5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN CREBBP IN COMPLEX REMARK 900 WITH AN ISOXAZOLYL-BENZIMIDAZOLE LIGAND DBREF 6DMK A 1083 1195 UNP Q92793 CBP_HUMAN 1045 1157 SEQRES 1 A 113 LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU MET SEQRES 2 A 113 PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SER SEQRES 3 A 113 LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU GLY SEQRES 4 A 113 ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET ASP SEQRES 5 A 113 LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN TYR SEQRES 6 A 113 GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU MET SEQRES 7 A 113 PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER ARG SEQRES 8 A 113 VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE GLU SEQRES 9 A 113 GLN GLU ILE ASP PRO VAL MET GLN SER HET NO3 A1201 4 HET 2LL A1202 124 HET EDO A1203 10 HETNAM NO3 NITRATE ION HETNAM 2LL 5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-1-[2-(MORPHOLIN-4-YL) HETNAM 2 2LL ETHYL]-2-(2-PHENYLETHYL)-1H-BENZIMIDAZOLE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NO3 N O3 1- FORMUL 3 2LL C26 H30 N4 O2 FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *80(H2 O) HELIX 1 AA1 LYS A 1086 ARG A 1103 1 18 HELIX 2 AA2 SER A 1108 ARG A 1112 5 5 HELIX 3 AA3 ASP A 1116 GLY A 1121 1 6 HELIX 4 AA4 ASP A 1124 VAL A 1129 1 6 HELIX 5 AA5 ASP A 1134 THR A 1144 1 11 HELIX 6 AA6 GLU A 1149 ASN A 1168 1 20 HELIX 7 AA7 SER A 1172 SER A 1195 1 24 CISPEP 1 ASP A 1105 PRO A 1106 0 18.33 SITE 1 AC1 5 LEU A1109 PRO A1110 ARG A1173 2LL A1202 SITE 2 AC1 5 HOH A1317 SITE 1 AC2 15 PRO A1110 VAL A1115 LEU A1119 LEU A1120 SITE 2 AC2 15 TRP A1158 TRP A1165 ASN A1168 LYS A1170 SITE 3 AC2 15 VAL A1174 TYR A1175 NO3 A1201 EDO A1203 SITE 4 AC2 15 HOH A1302 HOH A1314 HOH A1360 SITE 1 AC3 4 TRP A1165 TYR A1175 2LL A1202 HOH A1302 CRYST1 24.697 44.311 52.916 90.00 95.87 90.00 P 1 21 1 2 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 0.040491 0.000000 0.004163 0.00000 SCALE2 0.000000 0.022568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018997 0.00000