HEADER TRANSCRIPTION 24-MAR-22 7UGI TITLE BROMODOMAIN OF EP300 LIGANDED WITH BMS-536924 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE ACETYLTRANSFERASE P300; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: P300 HAT,E1A-ASSOCIATED PROTEIN P300,HISTONE COMPND 5 BUTYRYLTRANSFERASE P300,HISTONE CROTONYLTRANSFERASE P300,PROTEIN 2- COMPND 6 HYDROXYISOBUTYRYLTRANSFERASE P300,PROTEIN LACTYLTRANSFERAS P300, COMPND 7 PROTEIN PROPIONYLTRANSFERASE P300; COMPND 8 EC: 2.3.1.48,2.3.1.-; COMPND 9 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: EP300, P300; 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 7UGI 1 REMARK REVDAT 1 12-APR-23 7UGI 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 1.16_3549 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) : 45.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 20771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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 45.1480 - 3.8251 0.95 2946 156 0.1731 0.2219 REMARK 3 2 3.8251 - 3.0363 1.00 2902 152 0.1966 0.2665 REMARK 3 3 3.0363 - 2.6525 0.99 2802 148 0.2340 0.2856 REMARK 3 4 2.6525 - 2.4100 0.99 2776 146 0.2423 0.3137 REMARK 3 5 2.4100 - 2.2373 0.99 2811 148 0.2655 0.3433 REMARK 3 6 2.2373 - 2.1054 0.99 2756 145 0.3037 0.3548 REMARK 3 7 2.1054 - 2.0000 0.99 2739 144 0.3440 0.3915 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.33 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): -27.5418 2.5507 23.2389 REMARK 3 T TENSOR REMARK 3 T11: 0.2964 T22: 0.2736 REMARK 3 T33: 0.3114 T12: 0.0231 REMARK 3 T13: -0.0319 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.1571 L22: 1.1293 REMARK 3 L33: 2.9229 L12: -0.1311 REMARK 3 L13: -0.1869 L23: 1.3763 REMARK 3 S TENSOR REMARK 3 S11: -0.0702 S12: 0.0100 S13: 0.0517 REMARK 3 S21: 0.0060 S22: 0.1049 S23: -0.0133 REMARK 3 S31: -0.0746 S32: -0.0554 S33: -0.0317 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 7UGI 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_1000264150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.0 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20775 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 5BT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M POTASSIUM PHOSPHATE MONOBASIC REMARK 280 20% W/V POLYETHYLENE GLYCOL 8,000, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.29667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 180.59333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 180.59333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.29667 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 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 B1348 LIES ON A SPECIAL POSITION. 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 ARG A1133 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1137 CG CD NE CZ NH1 NH2 REMARK 470 LYS B1050 CG 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 HOH A 1350 O HOH A 1360 2.19 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 B1359 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B1360 DISTANCE = 6.71 ANGSTROMS DBREF 7UGI A 1048 1161 UNP Q09472 EP300_HUMAN 1048 1161 DBREF 7UGI B 1048 1161 UNP Q09472 EP300_HUMAN 1048 1161 SEQADV 7UGI SER A -2 UNP Q09472 EXPRESSION TAG SEQADV 7UGI MET A -1 UNP Q09472 EXPRESSION TAG SEQADV 7UGI SER B -2 UNP Q09472 EXPRESSION TAG SEQADV 7UGI MET B -1 UNP Q09472 EXPRESSION TAG SEQRES 1 A 116 SER MET 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 SER 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 ILE 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 TYR CYS SER LYS LEU SER GLU VAL PHE SEQRES 9 A 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY SEQRES 1 B 116 SER MET 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 SER 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 ILE 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 TYR CYS SER LYS LEU SER GLU VAL PHE SEQRES 9 B 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY HET N6I A1201 60 HET PE5 A1202 27 HET EDO A1203 4 HET EDO A1204 4 HET EDO A1205 4 HET EDO A1206 4 HET EDO A1207 4 HET EDO A1208 4 HET EDO A1209 4 HET N6I B1201 60 HET EDO B1202 4 HET EDO B1203 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 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL HETNAM EDO 1,2-ETHANEDIOL HETSYN PE5 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETSYN 2 PE5 ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL; POLYETHYLENE HETSYN 3 PE5 GLYCOL PEG400 HETSYN EDO ETHYLENE GLYCOL FORMUL 3 N6I 2(C25 H26 CL N5 O3) FORMUL 4 PE5 C18 H38 O9 FORMUL 5 EDO 9(C2 H6 O2) FORMUL 15 HOH *120(H2 O) HELIX 1 AA1 LYS A 1050 ARG A 1067 1 18 HELIX 2 AA2 SER A 1072 ARG A 1076 5 5 HELIX 3 AA3 ASP A 1080 GLY A 1085 1 6 HELIX 4 AA4 ASP A 1088 VAL A 1093 1 6 HELIX 5 AA5 ASP A 1098 THR A 1108 1 11 HELIX 6 AA6 GLU A 1113 ASN A 1132 1 20 HELIX 7 AA7 SER A 1136 GLY A 1161 1 26 HELIX 8 AA8 LYS B 1050 ARG B 1067 1 18 HELIX 9 AA9 SER B 1072 ARG B 1076 5 5 HELIX 10 AB1 ASP B 1088 VAL B 1093 1 6 HELIX 11 AB2 ASP B 1098 GLY B 1109 1 12 HELIX 12 AB3 GLU B 1113 ASN B 1132 1 20 HELIX 13 AB4 SER B 1136 GLY B 1161 1 26 CISPEP 1 ASP A 1069 PRO A 1070 0 11.57 CISPEP 2 ASP B 1069 PRO B 1070 0 14.28 CRYST1 43.230 43.230 270.890 90.00 90.00 120.00 P 31 2 1 12 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 0.023132 0.013355 0.000000 0.00000 SCALE2 0.000000 0.026711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003692 0.00000