HEADER TRANSCRIPTION 24-MAR-22 7UGE TITLE BROMODOMAIN OF CBP LIGANDED WITH BMS-536924 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE ACETYLTRANSFERASE; COMPND 3 CHAIN: A, B; 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, SMALL MOLECULE LIGAND, COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHONBRUNN,M.BIKOWITZ REVDAT 2 25-OCT-23 7UGE 1 REMARK REVDAT 1 12-APR-23 7UGE 0 JRNL AUTH E.SCHONBRUNN,M.BIKOWITZ JRNL TITL STRUCTURAL BASIS OF CBP AND EP300 INTERACTION WITH KINASE JRNL TITL 2 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 17915 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 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 39.8290 - 4.0059 0.99 2200 140 0.1540 0.1572 REMARK 3 2 4.0059 - 3.1801 0.99 2134 143 0.1529 0.1901 REMARK 3 3 3.1801 - 2.7782 0.99 2146 140 0.1779 0.2158 REMARK 3 4 2.7782 - 2.5242 0.98 2100 127 0.1773 0.2028 REMARK 3 5 2.5242 - 2.3433 0.97 2088 136 0.1685 0.2287 REMARK 3 6 2.3433 - 2.2052 0.97 2091 138 0.1663 0.2120 REMARK 3 7 2.2052 - 2.0947 0.97 2060 132 0.1671 0.2128 REMARK 3 8 2.0947 - 2.0040 0.94 2014 126 0.1791 0.2375 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) : 19.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.66 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.6585 8.9858 -20.8517 REMARK 3 T TENSOR REMARK 3 T11: 0.1488 T22: 0.1353 REMARK 3 T33: 0.1566 T12: -0.0114 REMARK 3 T13: -0.0094 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.9821 L22: 0.3711 REMARK 3 L33: 0.4838 L12: -0.0710 REMARK 3 L13: -0.2864 L23: 0.0990 REMARK 3 S TENSOR REMARK 3 S11: 0.0472 S12: -0.0175 S13: 0.0173 REMARK 3 S21: 0.0100 S22: -0.0102 S23: 0.0028 REMARK 3 S31: -0.0141 S32: 0.0223 S33: -0.0346 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 7UGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000264133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17935 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 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 : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7KPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 BIS-TRIS PH6.5, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 29.64650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 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 A1419 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH B1397 DISTANCE = 6.24 ANGSTROMS DBREF 7UGE A 1082 1197 UNP I3L466 I3L466_HUMAN 617 732 DBREF 7UGE B 1082 1197 UNP I3L466 I3L466_HUMAN 617 732 SEQRES 1 A 116 LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU SEQRES 2 A 116 MET PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SEQRES 3 A 116 SER LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU SEQRES 4 A 116 GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET SEQRES 5 A 116 ASP LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN SEQRES 6 A 116 TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU SEQRES 7 A 116 MET PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER SEQRES 8 A 116 ARG VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE SEQRES 9 A 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY SEQRES 1 B 116 LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU SEQRES 2 B 116 MET PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SEQRES 3 B 116 SER LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU SEQRES 4 B 116 GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET SEQRES 5 B 116 ASP LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN SEQRES 6 B 116 TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU SEQRES 7 B 116 MET PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER SEQRES 8 B 116 ARG VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE SEQRES 9 B 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY HET N6I A1201 34 HET N6I B1201 34 HET EDO B1202 4 HETNAM N6I (3M)-4-{[(2S)-2-(3-CHLOROPHENYL)-2-HYDROXYETHYL]AMINO}- HETNAM 2 N6I 3-[4-METHYL-6-(MORPHOLIN-4-YL)-1H-BENZIMIDAZOL-2- HETNAM 3 N6I YL]PYRIDIN-2(1H)-ONE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 N6I 2(C25 H26 CL N5 O3) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *216(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 GLY A 1145 1 12 HELIX 6 AA6 PRO A 1150 ASN A 1168 1 19 HELIX 7 AA7 SER A 1172 GLY A 1197 1 26 HELIX 8 AA8 LYS B 1086 ARG B 1103 1 18 HELIX 9 AA9 SER B 1108 ARG B 1112 5 5 HELIX 10 AB1 ASP B 1116 GLY B 1121 1 6 HELIX 11 AB2 ASP B 1124 VAL B 1129 1 6 HELIX 12 AB3 ASP B 1134 THR B 1144 1 11 HELIX 13 AB4 GLU B 1149 ASN B 1168 1 20 HELIX 14 AB5 SER B 1172 GLY B 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 8.05 CISPEP 2 ASP B 1105 PRO B 1106 0 9.83 CRYST1 43.122 59.293 57.147 90.00 109.81 90.00 P 1 21 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 0.023190 0.000000 0.008353 0.00000 SCALE2 0.000000 0.016865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018599 0.00000