HEADER GENE REGULATION/INHIBITOR 07-JAN-21 7LB4 TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN BRD3 BOUND TITLE 2 TO BROMOSPORINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RING3-LIKE 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: BRD3, KIAA0043, RING3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BET, ERK5, DUAL BRD-KINASE INHIBITOR, GENE REGULATION, GENE KEYWDS 2 REGULATION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,M.J.BIKOWITZ,E.SCHONBRUNN REVDAT 4 18-OCT-23 7LB4 1 REMARK REVDAT 3 24-NOV-21 7LB4 1 JRNL REVDAT 2 17-NOV-21 7LB4 1 JRNL REVDAT 1 14-JUL-21 7LB4 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 38.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 15400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1062 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 38.1350 - 4.0059 1.00 1888 134 0.1585 0.2027 REMARK 3 2 4.0059 - 3.1801 1.00 1847 139 0.1593 0.1815 REMARK 3 3 3.1801 - 2.7783 0.99 1814 133 0.2012 0.2515 REMARK 3 4 2.7783 - 2.5243 0.98 1789 130 0.1993 0.2558 REMARK 3 5 2.5243 - 2.3434 0.97 1791 133 0.1879 0.2468 REMARK 3 6 2.3434 - 2.2052 0.97 1779 133 0.1857 0.2887 REMARK 3 7 2.2052 - 2.0948 0.97 1733 129 0.1992 0.2582 REMARK 3 8 2.0948 - 2.0040 0.93 1697 131 0.2250 0.3271 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 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): -14.6690 16.0599 -15.3597 REMARK 3 T TENSOR REMARK 3 T11: 0.2030 T22: 0.1725 REMARK 3 T33: 0.1967 T12: -0.0118 REMARK 3 T13: -0.0025 T23: 0.0359 REMARK 3 L TENSOR REMARK 3 L11: 0.8638 L22: 1.0599 REMARK 3 L33: 1.9440 L12: -0.2790 REMARK 3 L13: -0.2796 L23: 1.1064 REMARK 3 S TENSOR REMARK 3 S11: -0.0394 S12: 0.0010 S13: -0.0139 REMARK 3 S21: -0.0195 S22: 0.0806 S23: 0.0053 REMARK 3 S31: -0.0619 S32: 0.0038 S33: -0.0432 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 7LB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-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) : 1.000 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15413 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 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: 7L9L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 10 % W/V REMARK 280 POLYETHYLENE GLYCOL 6,000, 5 % V/V (+/-)-2-METHYL-2,4- REMARK 280 PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 23.81900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 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 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 304 REMARK 465 MET A 305 REMARK 465 GLY A 306 REMARK 465 LYS A 307 REMARK 465 LEU A 308 REMARK 465 SER B 304 REMARK 465 MET B 305 REMARK 465 GLY B 306 REMARK 465 LYS B 307 REMARK 465 LEU B 308 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 603 O HOH A 663 2.16 REMARK 500 O HOH A 644 O HOH B 638 2.17 REMARK 500 O HOH A 663 O HOH A 664 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 BMF B 501 DBREF 7LB4 A 306 416 UNP Q15059 BRD3_HUMAN 306 416 DBREF 7LB4 B 306 416 UNP Q15059 BRD3_HUMAN 306 416 SEQADV 7LB4 SER A 304 UNP Q15059 EXPRESSION TAG SEQADV 7LB4 MET A 305 UNP Q15059 EXPRESSION TAG SEQADV 7LB4 SER B 304 UNP Q15059 EXPRESSION TAG SEQADV 7LB4 MET B 305 UNP Q15059 EXPRESSION TAG SEQRES 1 A 113 SER MET GLY LYS LEU SER GLU HIS LEU ARG TYR CYS ASP SEQRES 2 A 113 SER ILE LEU ARG GLU MET LEU SER LYS LYS HIS ALA ALA SEQRES 3 A 113 TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA GLU ALA SEQRES 4 A 113 LEU GLU LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO SEQRES 5 A 113 MET ASP LEU SER THR VAL LYS ARG LYS MET ASP GLY ARG SEQRES 6 A 113 GLU TYR PRO ASP ALA GLN GLY PHE ALA ALA ASP VAL ARG SEQRES 7 A 113 LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP SEQRES 8 A 113 HIS GLU VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL SEQRES 9 A 113 PHE GLU MET ARG PHE ALA LYS MET PRO SEQRES 1 B 113 SER MET GLY LYS LEU SER GLU HIS LEU ARG TYR CYS ASP SEQRES 2 B 113 SER ILE LEU ARG GLU MET LEU SER LYS LYS HIS ALA ALA SEQRES 3 B 113 TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA GLU ALA SEQRES 4 B 113 LEU GLU LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO SEQRES 5 B 113 MET ASP LEU SER THR VAL LYS ARG LYS MET ASP GLY ARG SEQRES 6 B 113 GLU TYR PRO ASP ALA GLN GLY PHE ALA ALA ASP VAL ARG SEQRES 7 B 113 LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP SEQRES 8 B 113 HIS GLU VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL SEQRES 9 B 113 PHE GLU MET ARG PHE ALA LYS MET PRO HET BMF A 501 28 HET BMF B 501 28 HETNAM BMF BROMOSPORINE 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 FORMUL 3 BMF 2(C17 H20 N6 O4 S) FORMUL 5 HOH *131(H2 O) HELIX 1 AA1 SER A 309 LEU A 323 1 15 HELIX 2 AA2 SER A 324 LYS A 326 5 3 HELIX 3 AA3 HIS A 327 TRP A 332 1 6 HELIX 4 AA4 PRO A 333 TYR A 335 5 3 HELIX 5 AA5 ASP A 339 GLU A 344 1 6 HELIX 6 AA6 ASP A 347 ILE A 352 1 6 HELIX 7 AA7 ASP A 357 GLY A 367 1 11 HELIX 8 AA8 ASP A 372 ASN A 391 1 20 HELIX 9 AA9 HIS A 395 LYS A 414 1 20 HELIX 10 AB1 GLU B 310 SER B 324 1 15 HELIX 11 AB2 HIS B 327 TRP B 332 1 6 HELIX 12 AB3 PRO B 333 TYR B 335 5 3 HELIX 13 AB4 ASP B 339 GLU B 344 1 6 HELIX 14 AB5 ASP B 347 ILE B 352 1 6 HELIX 15 AB6 ASP B 357 GLY B 367 1 11 HELIX 16 AB7 ASP B 372 ASN B 391 1 20 HELIX 17 AB8 HIS B 395 LYS B 414 1 20 SITE 1 AC1 12 TRP A 332 PRO A 333 LYS A 336 PRO A 337 SITE 2 AC1 12 VAL A 338 ASP A 339 LEU A 343 LEU A 345 SITE 3 AC1 12 ASN A 391 HIS A 395 HOH A 604 HOH A 608 SITE 1 AC2 11 TRP B 332 PRO B 333 LYS B 336 PRO B 337 SITE 2 AC2 11 VAL B 338 ASP B 339 LEU B 343 ASN B 391 SITE 3 AC2 11 VAL B 397 HOH B 608 HOH B 623 CRYST1 40.062 47.638 64.728 90.00 107.84 90.00 P 1 21 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 0.024961 0.000000 0.008034 0.00000 SCALE2 0.000000 0.020992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016230 0.00000