HEADER TRANSCRIPTION 26-JAN-22 7QWY TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH ACETYLPYRROLE DERIVATIVE COMPOUND 61 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 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 7QWY 1 REMARK REVDAT 1 28-SEP-22 7QWY 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. 2.44 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 6406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.430 REMARK 3 FREE R VALUE TEST SET COUNT : 284 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 47.1830 - 3.0779 1.00 3120 150 0.1983 0.2275 REMARK 3 2 3.0779 - 2.4431 0.99 3002 134 0.2896 0.3470 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.27 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 : 0.008 908 REMARK 3 ANGLE : 1.048 1224 REMARK 3 CHIRALITY : 0.050 120 REMARK 3 PLANARITY : 0.005 160 REMARK 3 DIHEDRAL : 12.864 537 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 7QWY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292120570. 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 : 6468 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 47.183 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 17.10 REMARK 200 R MERGE FOR SHELL (I) : 1.37600 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 (%): 64.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 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 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 11.02100 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 22.04200 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 22.04200 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 11.02100 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: 6510 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1794 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QVU RELATED DB: PDB REMARK 900 7QVU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QWU RELATED DB: PDB REMARK 900 7QWU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QWF RELATED DB: PDB REMARK 900 7QWF CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. DBREF 7QWY A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 7QWY SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QWY MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQRES 1 A 105 SER MET HIS SER ASP LEU THR PHE CYS GLU ILE ILE LEU SEQRES 2 A 105 MET GLU MET GLU SER HIS ASP ALA ALA TRP PRO PHE LEU SEQRES 3 A 105 GLU PRO VAL ASN PRO ARG LEU VAL SER GLY TYR ARG ARG SEQRES 4 A 105 ILE ILE LYS ASN PRO MET ASP PHE SER THR MET ARG GLU SEQRES 5 A 105 ARG LEU LEU ARG GLY GLY TYR THR SER SER GLU GLU PHE SEQRES 6 A 105 ALA ALA ASP ALA LEU LEU VAL PHE ASP ASN CYS GLN THR SEQRES 7 A 105 PHE ASN GLU ASP ASP SER GLU VAL GLY LYS ALA GLY HIS SEQRES 8 A 105 ILE MET ARG ARG PHE PHE GLU SER ARG TRP GLU GLU PHE SEQRES 9 A 105 TYR HET G0I A1901 23 HETNAM G0I 1-[4-ETHYL-2-METHYL-5-[2-(PIPERAZIN-1-YLMETHYL)-1,3- HETNAM 2 G0I THIAZOL-4-YL]-1~{H}-PYRROL-3-YL]ETHANONE FORMUL 2 G0I C17 H24 N4 O S FORMUL 3 HOH *12(H2 O) HELIX 1 AA1 MET A 1795 HIS A 1812 1 18 HELIX 2 AA2 ASP A 1813 LEU A 1819 5 7 HELIX 3 AA3 GLY A 1829 ILE A 1834 1 6 HELIX 4 AA4 ASP A 1839 GLY A 1850 1 12 HELIX 5 AA5 SER A 1854 ASN A 1873 1 20 HELIX 6 AA6 SER A 1877 GLU A 1896 1 20 CRYST1 94.365 94.365 33.063 90.00 90.00 120.00 P 31 2 1 6 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 0.010597 0.006118 0.000000 0.00000 SCALE2 0.000000 0.012237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030245 0.00000