HEADER TRANSCRIPTION 28-JAN-22 7QYO TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH ACETYLPYRROLE DERIVATIVE COMPOUND 79 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (RESIDUES 1796-1899); COMPND 5 SYNONYM: TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5, COMPND 6 TTF-I-INTERACTING PROTEIN 5,TIP5,HWALP3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAZ2A, KIAA0314, TIP5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,G.CAZZANELLI,A.CAFLISCH,G.LOLLI REVDAT 2 31-JAN-24 7QYO 1 REMARK REVDAT 1 28-SEP-22 7QYO 0 JRNL AUTH A.DALLE VEDOVE,G.CAZZANELLI,L.BATISTE,J.R.MARCHAND, JRNL AUTH 2 D.SPILIOTOPOULOS,J.CORSI,V.G.D'AGOSTINO,A.CAFLISCH,G.LOLLI JRNL TITL IDENTIFICATION OF A BAZ2A-BROMODOMAIN HIT COMPOUND BY JRNL TITL 2 FRAGMENT GROWING. JRNL REF ACS MED.CHEM.LETT. V. 13 1434 2022 JRNL REFN ISSN 1948-5875 JRNL PMID 36105334 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00173 REMARK 2 REMARK 2 RESOLUTION. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1 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) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 55440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.136 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 2836 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 27.3200 - 2.6682 0.99 2707 147 0.1427 0.1355 REMARK 3 2 2.6682 - 2.1181 0.99 2661 142 0.1399 0.1322 REMARK 3 3 2.1181 - 1.8504 0.99 2646 128 0.1317 0.1417 REMARK 3 4 1.8504 - 1.6812 0.99 2685 109 0.1360 0.1380 REMARK 3 5 1.6812 - 1.5608 0.99 2676 89 0.1185 0.1173 REMARK 3 6 1.5608 - 1.4687 1.00 2664 130 0.1155 0.1290 REMARK 3 7 1.4687 - 1.3952 1.00 2601 170 0.1156 0.1358 REMARK 3 8 1.3952 - 1.3345 1.00 2604 198 0.1126 0.1424 REMARK 3 9 1.3345 - 1.2831 1.00 2585 199 0.1138 0.1246 REMARK 3 10 1.2831 - 1.2388 1.00 2660 141 0.1161 0.1304 REMARK 3 11 1.2388 - 1.2001 1.00 2582 164 0.1123 0.1335 REMARK 3 12 1.2001 - 1.1658 1.00 2623 158 0.1098 0.1366 REMARK 3 13 1.1658 - 1.1351 1.00 2634 139 0.1117 0.1387 REMARK 3 14 1.1351 - 1.1074 0.99 2635 137 0.1139 0.1332 REMARK 3 15 1.1074 - 1.0822 0.99 2608 144 0.1207 0.1356 REMARK 3 16 1.0822 - 1.0592 0.99 2626 112 0.1237 0.1314 REMARK 3 17 1.0592 - 1.0380 0.99 2609 148 0.1276 0.1361 REMARK 3 18 1.0380 - 1.0184 0.98 2599 146 0.1396 0.1545 REMARK 3 19 1.0184 - 1.0002 0.99 2613 127 0.1501 0.1832 REMARK 3 20 1.0002 - 0.9833 0.97 2586 108 0.1806 0.1908 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.69 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 : 0.008 1050 REMARK 3 ANGLE : 1.354 1435 REMARK 3 CHIRALITY : 0.267 132 REMARK 3 PLANARITY : 0.006 191 REMARK 3 DIHEDRAL : 33.007 419 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 7QYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-19 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9133 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55493 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 37.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 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: PHASER REMARK 200 STARTING MODEL: 5MGJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M MGCL2, PH 7.5, REMARK 280 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 17.53400 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6650 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QXL RELATED DB: PDB REMARK 900 7QXL CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QYE RELATED DB: PDB REMARK 900 7QYE CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. DBREF 7QYO A 1796 1899 UNP Q9UIF9 BAZ2A_HUMAN 1796 1899 SEQADV 7QYO SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QYO MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QYO HIS A 1845 UNP Q9UIF9 GLU 1845 ENGINEERED MUTATION SEQADV 7QYO SER A 1848 UNP Q9UIF9 LEU 1848 ENGINEERED MUTATION SEQRES 1 A 106 SER MET HIS SER ASP LEU THR PHE CYS GLU ILE ILE LEU SEQRES 2 A 106 MET GLU MET GLU SER HIS ASP ALA ALA TRP PRO PHE LEU SEQRES 3 A 106 GLU PRO VAL ASN PRO ARG LEU VAL SER GLY TYR ARG ARG SEQRES 4 A 106 ILE ILE LYS ASN PRO MET ASP PHE SER THR MET ARG HIS SEQRES 5 A 106 ARG LEU SER ARG GLY GLY TYR THR SER SER GLU GLU PHE SEQRES 6 A 106 ALA ALA ASP ALA LEU LEU VAL PHE ASP ASN CYS GLN THR SEQRES 7 A 106 PHE ASN GLU ASP ASP SER GLU VAL GLY LYS ALA GLY HIS SEQRES 8 A 106 ILE MET ARG ARG PHE PHE GLU SER ARG TRP GLU GLU PHE SEQRES 9 A 106 TYR GLN HET GKI A1901 106 HET GKI A1902 53 HETNAM GKI 1-[2-METHYL-4-(3-METHYLBUTYL)-5-(2-PIPERAZIN-1-YL-1,3- HETNAM 2 GKI THIAZOL-4-YL)-1~{H}-PYRROL-3-YL]ETHANONE FORMUL 2 GKI 2(C19 H28 N4 O S) FORMUL 4 HOH *168(H2 O) HELIX 1 AA1 HIS A 1796 ASP A 1798 5 3 HELIX 2 AA2 LEU A 1799 HIS A 1812 1 14 HELIX 3 AA3 ALA A 1815 LEU A 1819 5 5 HELIX 4 AA4 GLY A 1829 ILE A 1834 1 6 HELIX 5 AA5 ASP A 1839 GLY A 1850 1 12 HELIX 6 AA6 SER A 1854 ASN A 1873 1 20 HELIX 7 AA7 SER A 1877 TYR A 1898 1 22 CRYST1 37.390 35.068 37.910 90.00 93.05 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 0.026745 0.000000 0.001426 0.00000 SCALE2 0.000000 0.028516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026416 0.00000