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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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