HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 05-JUN-18 6DMJ TITLE A MULTICONFORMER LIGAND MODEL OF INHIBITOR 53W BOUND TO CREB BINDING TITLE 2 PROTEIN BROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, MULTICONFORMER MODEL, INHIBITOR, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.HUDSON,G.VAN ZUNDERT,D.KEEDY,R.FONSECA,A.HELIOU,P.SURESH, AUTHOR 2 K.BORRELLI,T.DAY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 3 13-MAR-24 6DMJ 1 REMARK REVDAT 2 24-APR-19 6DMJ 1 JRNL REVDAT 1 19-DEC-18 6DMJ 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 6DMJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 5CFW, DETERMINED BY E.L.CHEKLER,J.A.PELLEGRINO,T.A.LANZ, REMARK 0 R.A.DENNY,A.C.FLICK,J.COE,J.LANGILLE,A.BASAK,S.LIU,I.A.STOCK, REMARK 0 P.SAHASRABUDHE,P.D.BONIN,K.LEE,M.T.PLETCHER,L.H.JONES REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.L.CHEKLER,J.A.PELLEGRINO,T.A.LANZ,R.A.DENNY,A.C.FLICK, REMARK 1 AUTH 2 J.COE,J.LANGILLE,A.BASAK,S.LIU,I.A.STOCK,P.SAHASRABUDHE, REMARK 1 AUTH 3 P.D.BONIN,K.LEE,M.T.PLETCHER,L.H.JONES REMARK 1 TITL TRANSCRIPTIONAL PROFILING OF A SELECTIVE CREB BINDING REMARK 1 TITL 2 PROTEIN BROMODOMAIN INHIBITOR HIGHLIGHTS THERAPEUTIC REMARK 1 TITL 3 OPPORTUNITIES. REMARK 1 REF CHEM. BIOL. V. 22 1588 2015 REMARK 1 REFN ISSN 1879-1301 REMARK 1 PMID 26670081 REMARK 1 DOI 10.1016/J.CHEMBIOL.2015.10.013 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 37922 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1894 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 13.7575 - 2.7655 0.99 2971 138 0.1638 0.1939 REMARK 3 2 2.7655 - 2.1980 1.00 2829 169 0.1646 0.1929 REMARK 3 3 2.1980 - 1.9210 0.99 2813 160 0.1392 0.1626 REMARK 3 4 1.9210 - 1.7457 0.99 2782 141 0.1537 0.2299 REMARK 3 5 1.7457 - 1.6208 1.00 2792 149 0.1462 0.1855 REMARK 3 6 1.6208 - 1.5254 1.00 2757 148 0.1407 0.1704 REMARK 3 7 1.5254 - 1.4491 0.99 2790 137 0.1446 0.1851 REMARK 3 8 1.4491 - 1.3860 1.00 2771 147 0.1498 0.1905 REMARK 3 9 1.3860 - 1.3327 1.00 2736 151 0.1594 0.2004 REMARK 3 10 1.3327 - 1.2868 1.00 2743 141 0.1648 0.2125 REMARK 3 11 1.2868 - 1.2466 0.92 2554 131 0.1847 0.2631 REMARK 3 12 1.2466 - 1.2110 0.79 2182 118 0.1864 0.2334 REMARK 3 13 1.2110 - 1.1791 0.66 1798 99 0.2097 0.2128 REMARK 3 14 1.1791 - 1.1503 0.54 1510 65 0.2198 0.2676 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.26 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 : 0.020 1185 REMARK 3 ANGLE : 1.810 1621 REMARK 3 CHIRALITY : 0.096 161 REMARK 3 PLANARITY : 0.013 205 REMARK 3 DIHEDRAL : 21.054 452 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 6DMJ 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_1000234876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-12 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37951 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 31.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 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: BUSTER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 5CFW REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.80500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.60500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.60500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.80500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.13500 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 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 A 112 CE NZ REMARK 470 LYS A 141 CD CE NZ 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 GLN A 127 CG GLN A 127 CD 0.218 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 53W A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CFW RELATED DB: PDB REMARK 900 SELECTIVE PHARMACOLOGICAL INHIBITION OF THE CREB BINDING PROTEIN REMARK 900 BROMODOMAIN REGULATES INFLAMMATORY CYTOKINES IN MACROPHAGES AND REMARK 900 RGS4 IN NEURONS DBREF 6DMJ A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6DMJ SER A 42 UNP O60885 EXPRESSION TAG SEQADV 6DMJ MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET 53W A 201 132 HETNAM 53W 5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2-[2-(4- HETNAM 2 53W METHOXYPHENYL)ETHYL]-1-[2-(MORPHOLIN-4-YL)ETHYL]-1H- HETNAM 3 53W BENZIMIDAZOLE FORMUL 2 53W C27 H32 N4 O3 FORMUL 3 HOH *177(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 SITE 1 AC1 14 GLN A 59 TRP A 81 PRO A 82 LYS A 91 SITE 2 AC1 14 LEU A 92 LEU A 94 ASN A 140 ASP A 145 SITE 3 AC1 14 MET A 149 GLU A 151 HOH A 309 HOH A 310 SITE 4 AC1 14 HOH A 337 HOH A 439 CRYST1 39.610 50.270 57.210 90.00 90.00 90.00 P 21 21 21 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 0.025246 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017479 0.00000