HEADER GENE REGULATION 23-DEC-20 7L6D TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN BRD2 BOUND TITLE 2 TO BROMOSPORINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BET, ERK5, DUAL BRD-KINASE INHIBITOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,M.J.BIKOWITZ,A.CHAN,E.SCHONBRUNN REVDAT 4 18-OCT-23 7L6D 1 REMARK REVDAT 3 24-NOV-21 7L6D 1 JRNL REVDAT 2 17-NOV-21 7L6D 1 JRNL REVDAT 1 23-JUN-21 7L6D 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 891 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 41.2500 - 2.8164 0.99 2889 153 0.1547 0.1579 REMARK 3 2 2.8164 - 2.2355 1.00 2843 149 0.1760 0.1852 REMARK 3 3 2.2355 - 1.9529 1.00 2819 149 0.1634 0.2165 REMARK 3 4 1.9529 - 1.7743 0.99 2815 148 0.1788 0.2228 REMARK 3 5 1.7743 - 1.6472 0.99 2798 147 0.1830 0.2143 REMARK 3 6 1.6472 - 1.5500 0.98 2749 145 0.2072 0.2668 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.65 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): -1.0802 1.8216 16.1768 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.0939 REMARK 3 T33: 0.0951 T12: -0.0090 REMARK 3 T13: 0.0322 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 2.6038 L22: 1.9021 REMARK 3 L33: 2.3141 L12: 0.2414 REMARK 3 L13: 0.9745 L23: 0.3053 REMARK 3 S TENSOR REMARK 3 S11: -0.0365 S12: 0.0914 S13: 0.0414 REMARK 3 S21: -0.0579 S22: -0.0040 S23: -0.0264 REMARK 3 S31: -0.0606 S32: 0.0350 S33: 0.0327 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 7L6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-19 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 41.254 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.790 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.82 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.810 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: 3ONI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PH 6.5, 25 % W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 42.13000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.13000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.78000 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 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 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 S SO4 A 510 LIES ON A SPECIAL POSITION. REMARK 375 O4 SO4 A 510 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 646 LIES ON A SPECIAL POSITION. 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 342 REMARK 465 MET A 343 REMARK 465 GLY A 344 REMARK 465 LYS A 345 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 A 698 DISTANCE = 6.29 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BMF 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 510 DBREF 7L6D A 344 455 UNP P25440 BRD2_HUMAN 344 455 SEQADV 7L6D SER A 342 UNP P25440 EXPRESSION TAG SEQADV 7L6D MET A 343 UNP P25440 EXPRESSION TAG SEQRES 1 A 114 SER MET GLY LYS LEU SER GLU GLN LEU LYS HIS CYS ASN SEQRES 2 A 114 GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA SEQRES 3 A 114 TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA SEQRES 4 A 114 LEU GLY LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO SEQRES 5 A 114 MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG SEQRES 6 A 114 ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG SEQRES 7 A 114 LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP SEQRES 8 A 114 HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL SEQRES 9 A 114 PHE GLU PHE ARG TYR ALA LYS MET PRO ASP HET BMF A 501 28 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET SO4 A 510 5 HETNAM BMF BROMOSPORINE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN BMF ETHYL (3-METHYL-6-{4-METHYL-3-[(METHYLSULFONYL) HETSYN 2 BMF AMINO]PHENYL}[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-8-YL) HETSYN 3 BMF CARBAMATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 BMF C17 H20 N6 O4 S FORMUL 3 EDO 8(C2 H6 O2) FORMUL 11 SO4 O4 S 2- FORMUL 12 HOH *98(H2 O) HELIX 1 AA1 SER A 347 LEU A 361 1 15 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 LYS A 452 1 20 SITE 1 AC1 14 TRP A 370 PRO A 371 LYS A 374 PRO A 375 SITE 2 AC1 14 VAL A 376 ASP A 377 LEU A 381 ASN A 429 SITE 3 AC1 14 EDO A 504 EDO A 506 EDO A 507 HOH A 612 SITE 4 AC1 14 HOH A 642 HOH A 651 SITE 1 AC2 4 TRP A 370 HIS A 433 EDO A 504 HOH A 643 SITE 1 AC3 7 ILE A 389 ILE A 390 LYS A 391 HIS A 392 SITE 2 AC3 7 ASN A 424 LYS A 427 ASP A 455 SITE 1 AC4 7 PRO A 375 THR A 398 ARG A 401 BMF A 501 SITE 2 AC4 7 EDO A 502 EDO A 506 HOH A 618 SITE 1 AC5 5 HIS A 387 ILE A 390 LYS A 391 PRO A 393 SITE 2 AC5 5 HOH A 641 SITE 1 AC6 7 LEU A 381 PRO A 393 THR A 398 BMF A 501 SITE 2 AC6 7 EDO A 504 HOH A 625 HOH A 643 SITE 1 AC7 5 ASP A 377 HIS A 392 BMF A 501 HOH A 616 SITE 2 AC7 5 HOH A 638 SITE 1 AC8 4 SER A 362 LYS A 363 LYS A 364 HOH A 653 SITE 1 AC9 3 ASP A 388 HOH A 641 HOH A 680 SITE 1 AD1 4 ASN A 354 GLU A 404 ARG A 406 HOH A 603 CRYST1 84.260 35.560 47.080 90.00 118.81 90.00 C 1 2 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 0.011868 0.000000 0.006526 0.00000 SCALE2 0.000000 0.028121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024240 0.00000