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Chemical substance (2) PDB-CCD (2) Gene (1) KEGG GENES (1) Protein sequence (3) UniProt (1) SWISS-PROT (1) PDBSTR (1) DNA sequence (2) EMBL (2) Protein domain (7) InterPro (5) PROSITE (2) All databases (15)
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HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 23-SEP-14 4WHW
TITLE DIRECT PHOTOCAPTURE OF BROMODOMAINS USING TROPOLONE CHEMICAL PROBES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 44-168;
COMPND 5 SYNONYM: PROTEIN HUNK1;
COMPND 6 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 BROMO DOMAIN, BRD4, INHIBITOR, TRANSCRIPTION-TRANSCRIPTION INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.C.HETT,E.L.PIATNITSKI CHEKLER,A.BASAK,P.D.BONIN,R.A.DENNY,
AUTHOR 2 A.C.FLICK,K.F.GEOGHEGAN,S.LIU,M.T.PLETCHER,R.P.ROBINSON,
AUTHOR 3 P.SAHASRABUDHE,S.SALTER,I.A.STOCK,L.H.JONES
REVDAT 2 27-DEC-23 4WHW 1 REMARK
REVDAT 1 28-OCT-15 4WHW 0
JRNL AUTH E.C.HETT,E.L.PIATNITSKI CHEKLER,A.BASAK,P.D.BONIN,R.A.DENNY,
JRNL AUTH 2 A.C.FLICK,K.F.GEOGHEGAN,S.LIU,M.T.PLETCHER,R.P.ROBINSON,
JRNL AUTH 3 P.SAHASRABUDHE,S.SALTER,I.A.STOCK,L.H.JONES
JRNL TITL DIRECT PHOTOCAPTURE OF BROMODOMAINS USING TROPOLONE CHEMICAL
JRNL TITL 2 PROBES
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.88
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 26262
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.201
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060
REMARK 3 FREE R VALUE TEST SET COUNT : 1330
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 13
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.40
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.29
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2533
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2042
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2408
REMARK 3 BIN R VALUE (WORKING SET) : 0.2023
REMARK 3 BIN FREE R VALUE : 0.2397
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.93
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 125
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1033
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 39
REMARK 3 SOLVENT ATOMS : 125
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.29
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.74
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.60950
REMARK 3 B22 (A**2) : -0.73870
REMARK 3 B33 (A**2) : 0.12920
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.145
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.060
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.060
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.057
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.058
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1142 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1584 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 393 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 32 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 186 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1142 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 137 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 1412 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.98
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.55
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.53
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -6.4932 9.3878 -16.4799
REMARK 3 T TENSOR
REMARK 3 T11: -0.1182 T22: -0.1070
REMARK 3 T33: -0.1193 T12: 0.0000
REMARK 3 T13: -0.0001 T23: 0.0167
REMARK 3 L TENSOR
REMARK 3 L11: 0.7640 L22: 0.8042
REMARK 3 L33: 0.8557 L12: -0.1544
REMARK 3 L13: -0.3891 L23: 0.2350
REMARK 3 S TENSOR
REMARK 3 S11: -0.0451 S12: -0.0724 S13: -0.0458
REMARK 3 S21: 0.0134 S22: -0.0064 S23: -0.0220
REMARK 3 S31: -0.0055 S32: 0.0472 S33: 0.0516
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4WHW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-14.
REMARK 100 THE DEPOSITION ID IS D_1000203846.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-NOV-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 17-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
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 : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26339
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.345
REMARK 200 RESOLUTION RANGE LOW (A) : 57.468
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 5.800
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35
REMARK 200 COMPLETENESS FOR SHELL (%) : 77.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : 0.45600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SCREEN USING HAMPTON RESEARCH HT AND
REMARK 280 INDEX KITS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 19.91500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.73400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.29550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.73400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.91500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.29550
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 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 42
REMARK 465 GLU A 167
REMARK 465 GLU A 168
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN A 59 CG CD OE1 NE2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 3OT A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202
DBREF 4WHW A 44 168 UNP O60885 BRD4_HUMAN 44 168
SEQADV 4WHW SER A 42 UNP O60885 EXPRESSION TAG
SEQADV 4WHW MET A 43 UNP O60885 INITIATING METHIONINE
SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN
SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU
SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA
SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN
SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP
SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR
SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET
SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP
SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU
SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU
HET 3OT A 201 66
HET EDO A 202 10
HETNAM 3OT 2-METHOXY-4-{1-[2-(MORPHOLIN-4-YL)ETHYL]-2-(2-
HETNAM 2 3OT PHENYLETHYL)-1H-BENZIMIDAZOL-5-YL}CYCLOHEPTA-2,4,6-
HETNAM 3 3OT TRIEN-1-ONE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 3OT C29 H31 N3 O3
FORMUL 3 EDO C2 H6 O2
FORMUL 4 HOH *125(H2 O)
HELIX 1 AA1 THR A 60 VAL A 69 1 10
HELIX 2 AA2 VAL A 69 LYS A 76 1 8
HELIX 3 AA3 ALA A 80 GLN A 84 5 5
HELIX 4 AA4 ASP A 88 ASN A 93 1 6
HELIX 5 AA5 ASP A 96 ILE A 101 1 6
HELIX 6 AA6 ASP A 106 ASN A 116 1 11
HELIX 7 AA7 ASN A 121 ASN A 140 1 20
HELIX 8 AA8 ASP A 144 ASN A 162 1 19
SITE 1 AC1 11 TRP A 81 PRO A 82 PHE A 83 VAL A 87
SITE 2 AC1 11 LEU A 92 LEU A 94 ASN A 140 ILE A 146
SITE 3 AC1 11 HOH A 369 HOH A 384 HOH A 400
SITE 1 AC2 5 ILE A 100 ILE A 101 LYS A 102 THR A 103
SITE 2 AC2 5 ASN A 135
CRYST1 39.830 50.591 57.468 90.00 90.00 90.00 P 21 21 21 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 0.025107 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019766 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017401 0.00000
(ATOM LINES ARE NOT SHOWN.)
END