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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH SB-251527
 
Authors :  S. W. Ember, J. -Y. Zhu, C. Watts, E. Schonbrunn
Date :  24 Dec 13  (Deposition) - 05 Mar 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bromodomain, Cap, Hunk1, Mcap, Protein Binding-Inhibitor Complex, Mitotic Chromosome Associated Protein, Cell Cycle, Inhibitor, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Ember, J. Y. Zhu, S. H. Olesen, M. P. Martin, A. Becker, N. Berndt, G. I. Georg, E. Schonbrunn
Acetyl-Lysine Binding Site Of Bromodomain-Containing Protei 4 (Brd4) Interacts With Diverse Kinase Inhibitors.
Acs Chem. Biol. V. 9 1160 2014
PubMed-ID: 24568369  |  Reference-DOI: 10.1021/CB500072Z

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 44-168
    Gene: BRD4, HUNK1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN HUNK1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
12RQ2Ligand/Ion4-[4-(4-FLUOROPHENYL)-1-(PIPERIDIN-4-YL)-1H-IMIDAZOL-5-YL]-2-(2-METHOXYPHENOXY)PYRIMIDINE
2CL1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12RQ1Ligand/Ion4-[4-(4-FLUOROPHENYL)-1-(PIPERIDIN-4-YL)-1H-IMIDAZOL-5-YL]-2-(2-METHOXYPHENOXY)PYRIMIDINE
2CL-1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
12RQ1Ligand/Ion4-[4-(4-FLUOROPHENYL)-1-(PIPERIDIN-4-YL)-1H-IMIDAZOL-5-YL]-2-(2-METHOXYPHENOXY)PYRIMIDINE
2CL-1Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:81 , PRO A:82 , PHE A:83 , VAL A:87 , LEU A:92 , TYR A:97 , MET A:132 , ASN A:140 , ILE A:146 , HOH A:308 , HOH A:373BINDING SITE FOR RESIDUE 2RQ A 201
2AC2SOFTWAREILE A:100 , ILE A:101 , LYS A:102 , THR A:103 , ASN A:135 , ASN B:116 , HOH B:368BINDING SITE FOR RESIDUE EDO A 202
3AC3SOFTWAREASP A:144 , ASP A:145 , HOH A:320BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWARETRP B:81 , PRO B:82 , PHE B:83 , TYR B:97 , MET B:132 , ASN B:140 , ILE B:146 , MET B:149 , HOH B:306 , HOH B:326 , HOH B:369BINDING SITE FOR RESIDUE 2RQ B 201
5AC5SOFTWAREILE B:100 , ILE B:101 , LYS B:102 , THR B:103 , ASN B:135BINDING SITE FOR RESIDUE EDO B 202
6AC6SOFTWARELEU B:92 , HOH B:360 , HOH B:367 , HOH B:399BINDING SITE FOR RESIDUE EDO B 203
7AC7SOFTWAREPRO A:45 , PRO A:46 , HOH A:365 , LYS B:55 , PRO B:56 , TYR B:118 , TRP B:120 , GLU B:124BINDING SITE FOR RESIDUE EDO B 204
8AC8SOFTWARELYS A:111 , LYS A:112 , GLU A:115 , HOH A:301 , ILE B:138 , TYR B:139 , ASN B:140 , LYS B:141BINDING SITE FOR RESIDUE EDO B 205
9AC9SOFTWAREPRO A:142 , LEU B:71 , LYS B:72 , HOH B:352 , HOH B:381BINDING SITE FOR RESIDUE EDO B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O7F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O7F)

(-) Exons   (0, 0)

(no "Exon" information available for 4O7F)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains d4o7fa_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o7f A  42 SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE 168
                                    51        61        71        81        91       101       111       121       131       141       151       161       


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains d4o7fb_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o7f B  42 SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE 168
                                    51        61        71        81        91       101       111       121       131       141       151       161
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O7F)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  4o7f
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  BRD4_HUMAN | O60885
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BRD4_HUMAN | O60885: 2i8n 2lsp 2mjv 2n3k 2ncz 2nd0 2nd1 2nnu 2oss 2ouo 2yel 2yem 3mxf 3p5o 3svf 3svg 3u5j 3u5k 3u5l 3uvw 3uvx 3uvy 3uw9 3zyu 4a9l 4bjx 4bw1 4bw2 4bw3 4bw4 4c66 4c67 4cfk 4cfl 4cl9 4clb 4don 4e96 4f3i 4gpj 4hbv 4hbw 4hbx 4hby 4hxk 4hxl 4hxm 4hxn 4hxo 4hxp 4hxr 4hxs 4ioo 4ioq 4ior 4j0r 4j0s 4j3i 4kv1 4kv4 4lr6 4lrg 4lyi 4lys 4lyw 4lzr 4lzs 4men 4meo 4mep 4meq 4mr3 4mr4 4nqm 4nr8 4nuc 4nud 4nue 4o70 4o71 4o72 4o74 4o75 4o76 4o77 4o78 4o7a 4o7b 4o7c 4o7e 4ogi 4ogj 4pce 4pci 4ps5 4qb3 4qr3 4qr4 4qr5 4qzs 4uix 4uiy 4uiz 4uyd 4whw 4wiv 4x2i 4xy9 4xya 4yh3 4yh4 4z1q 4z1s 4z93 4zc9 4zw1 5a5s 5a85 5acy 5ad2 5ad3 5bt4 5cfw 5coi 5cp5 5cpe 5cqt 5crm 5crz 5cs8 5ctl 5cy9 5d0c 5d24 5d25 5d26 5d3h 5d3j 5d3l 5d3n 5d3p 5d3r 5d3s 5d3t 5dlx 5dlz 5dw2 5dx4 5e0r 5egu 5ei4 5eis 5f5z 5f60 5f61 5f62 5f63 5fbx 5h21 5hcl 5hls 5hm0 5hq5 5hq6 5hq7 5i80 5i88 5igk 5jwm 5khm 5ku3 5lj1 5lj2 5luu 5t35 5u28 5u2c 5u2e 5u2f 5ueo 5uep 5ueq 5uer 5ues 5uet 5ueu 5uev 5uex 5uey 5uez 5uf0 5ula 5uoo 5uvs 5uvt 5uvu 5uvv 5uvw 5uvx 5uvy 5uvz 5wuu

(-) Related Entries Specified in the PDB File

4o70 4o71 4o72 4o73 4o74 4o75 4o76 4o77 4o78 4o7a 4o7b 4o7c 4o7e