HEADER GENE REGULATION 06-NOV-20 7KO0 TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN BRD4 BOUND TITLE 2 TO SG3-179 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 BET, ERK5, PLK1, DUAL BRD-KINASE INHIBITOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,J.Y.ZHU,E.SCHONBRUNN REVDAT 4 18-OCT-23 7KO0 1 REMARK REVDAT 3 24-NOV-21 7KO0 1 JRNL REVDAT 2 17-NOV-21 7KO0 1 JRNL REVDAT 1 20-OCT-21 7KO0 0 JRNL AUTH R.M.KARIM,M.J.BIKOWITZ,A.CHAN,J.Y.ZHU,D.GRASSIE,A.BECKER, JRNL AUTH 2 N.BERNDT,S.GUNAWAN,N.J.LAWRENCE,E.SCHONBRUNN JRNL TITL DIFFERENTIAL BET BROMODOMAIN INHIBITION BY JRNL TITL 2 DIHYDROPTERIDINONE AND PYRIMIDODIAZEPINONE KINASE JRNL TITL 3 INHIBITORS. JRNL REF J.MED.CHEM. V. 64 15772 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34710325 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01096 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 10500 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 526 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 33.3600 - 3.0155 1.00 2615 138 0.1620 0.1915 REMARK 3 2 3.0155 - 2.3937 1.00 2470 130 0.1936 0.1992 REMARK 3 3 2.3937 - 2.0912 1.00 2456 129 0.1660 0.1880 REMARK 3 4 2.0912 - 1.9000 0.99 2433 129 0.1883 0.2545 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.01 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 349 THROUGH 381 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6650 8.9422 -14.7955 REMARK 3 T TENSOR REMARK 3 T11: 0.1397 T22: 0.1495 REMARK 3 T33: 0.2013 T12: -0.0361 REMARK 3 T13: 0.0104 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 2.5929 L22: 7.2456 REMARK 3 L33: 4.6084 L12: -1.4225 REMARK 3 L13: 1.5097 L23: -2.7233 REMARK 3 S TENSOR REMARK 3 S11: -0.1831 S12: 0.0210 S13: 0.0429 REMARK 3 S21: 0.0171 S22: 0.0637 S23: -0.1525 REMARK 3 S31: -0.3139 S32: -0.0712 S33: 0.1025 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 382 THROUGH 437 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9723 -2.7775 -18.8691 REMARK 3 T TENSOR REMARK 3 T11: 0.1917 T22: 0.2016 REMARK 3 T33: 0.1677 T12: -0.0027 REMARK 3 T13: 0.0465 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 3.0917 L22: 5.9536 REMARK 3 L33: 2.1171 L12: -0.8766 REMARK 3 L13: 0.8556 L23: -1.9673 REMARK 3 S TENSOR REMARK 3 S11: 0.0683 S12: 0.2949 S13: 0.0238 REMARK 3 S21: -0.3024 S22: -0.0933 S23: -0.4018 REMARK 3 S31: 0.0172 S32: 0.1590 S33: 0.0547 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 438 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.8830 5.6037 -11.4149 REMARK 3 T TENSOR REMARK 3 T11: 0.1426 T22: 0.1701 REMARK 3 T33: 0.1985 T12: -0.0193 REMARK 3 T13: 0.0305 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 3.8380 L22: 8.0898 REMARK 3 L33: 8.7278 L12: -4.2966 REMARK 3 L13: 3.3269 L23: -4.4835 REMARK 3 S TENSOR REMARK 3 S11: -0.2346 S12: -0.2256 S13: 0.1689 REMARK 3 S21: 0.3046 S22: 0.1306 S23: 0.1932 REMARK 3 S31: -0.2180 S32: -0.3788 S33: 0.0389 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 7KO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-15 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 33.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.880 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.06 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.510 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: 4Z93 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 20% PEG 3,350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.32000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.32000 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 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 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 GLU A 460 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5W2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 DBREF 7KO0 A 349 460 UNP O60885 BRD4_HUMAN 349 460 SEQRES 1 A 112 LYS VAL SER GLU GLN LEU LYS CYS CYS SER GLY ILE LEU SEQRES 2 A 112 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 112 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 A 112 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 A 112 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 A 112 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 112 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 112 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 112 ARG PHE ALA LYS MET PRO ASP GLU HET 5W2 A 501 41 HET EDO A 502 4 HETNAM 5W2 4-[[4-[[3-(~{TERT}-BUTYLSULFONYLAMINO)-4-CHLORANYL- HETNAM 2 5W2 PHENYL]AMINO]-5-METHYL-PYRIMIDIN-2-YL]AMINO]-2- HETNAM 3 5W2 FLUORANYL-~{N}-(1-METHYLPIPERIDIN-4-YL)BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5W2 C28 H35 CL F N7 O3 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *63(H2 O) HELIX 1 AA1 LYS A 349 PHE A 365 1 17 HELIX 2 AA2 ALA A 366 LYS A 368 5 3 HELIX 3 AA3 HIS A 369 TRP A 374 1 6 HELIX 4 AA4 PRO A 375 TYR A 377 5 3 HELIX 5 AA5 ASP A 381 GLY A 386 1 6 HELIX 6 AA6 ASP A 389 ILE A 394 1 6 HELIX 7 AA7 ASP A 399 ALA A 409 1 11 HELIX 8 AA8 ASP A 414 ASN A 433 1 20 HELIX 9 AA9 HIS A 437 ALA A 455 1 19 SITE 1 AC1 11 LYS A 355 TRP A 374 PRO A 375 PHE A 376 SITE 2 AC1 11 VAL A 380 LEU A 385 ASN A 433 HIS A 437 SITE 3 AC1 11 GLU A 438 VAL A 439 HOH A 639 SITE 1 AC2 7 ILE A 393 ILE A 394 LYS A 395 HIS A 396 SITE 2 AC2 7 ASN A 428 LYS A 431 ASP A 459 CRYST1 52.400 72.640 33.360 90.00 90.00 90.00 P 21 21 2 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 0.019084 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029976 0.00000