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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIFTH BROMODOMAIN OF HUMAN PB1 IN COMPLEX WITH A HYDROXYPHENYL LIGAND
 
Authors :  P. Filippakopoulos, S. Picaud, F. Von Delft, C. H. Arrowsmith, A. Edwa C. Bountra, D. Owen, S. Knapp, Structural Genomics Consortium (Sg
Date :  12 Oct 15  (Deposition) - 12 Oct 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Bromodomain, Chemical Probe, Ligand, Inhibitor, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Filippakopoulos, S. Picaud, F. Von Delft, C. H. Arrowsmith, A. Edwards, C. Bountra, D. Owen, S. Knapp
Crystal Structure Of The Fifth Bromodomain Of Human Pb1 In Complex With A Hydroxyphenyl Ligand
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN POLYBROMO-1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 469008
    Expression System Variant: R3
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 645-766
    Gene: PBRM1, BAF180, PB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPB1,BRG1-ASSOCIATED FACTOR 180,BAF180,POLYBROMO-1D, PB1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
15KL4Ligand/Ion(2E)-3-(DIMETHYLAMINO)-1-(2-HYDROXYPHENYL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15KL1Ligand/Ion(2E)-3-(DIMETHYLAMINO)-1-(2-HYDROXYPHENYL)PROP-2-EN-1-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15KL1Ligand/Ion(2E)-3-(DIMETHYLAMINO)-1-(2-HYDROXYPHENYL)PROP-2-EN-1-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
15KL1Ligand/Ion(2E)-3-(DIMETHYLAMINO)-1-(2-HYDROXYPHENYL)PROP-2-EN-1-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
15KL1Ligand/Ion(2E)-3-(DIMETHYLAMINO)-1-(2-HYDROXYPHENYL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:651 , LEU A:655 , TYR A:664 , MET A:672 , ASN A:702 , ALA A:703 , ASN A:707 , ILE A:713 , EDO D:802binding site for residue 5KL A 801
2AC2SOFTWAREILE B:651 , PHE B:652 , LEU B:655 , LEU B:661 , TYR B:664 , MET B:672 , ALA B:703 , ASN B:707 , ILE B:713binding site for residue 5KL B 801
3AC3SOFTWAREILE C:651 , PHE C:652 , LEU C:655 , TYR C:664 , MET C:672 , ALA C:703 , ASN C:707 , ILE C:713binding site for residue 5KL C 801
4AC4SOFTWAREILE D:651 , PHE D:652 , LEU D:655 , TYR D:664 , MET D:672 , ALA D:703 , ASN D:707 , ILE D:713binding site for residue 5KL D 801
5AC5SOFTWARE5KL A:801 , ILE D:651 , ILE D:713 , ASP D:716 , HOH D:923 , HOH D:926binding site for residue EDO D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E7D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E7D)

(-) Exons   (0, 0)

(no "Exon" information available for 5E7D)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5e7d A 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730 


Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5e7d B 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730 


Chain C from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5e7d C 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730 


Chain D from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5e7d D 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 5E7D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E7D)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  5e7d
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  PB1_HUMAN | Q86U86
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 Related Entries

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UniProtKB/Swiss-Prot
        PB1_HUMAN | Q86U86: 2ktb 3g0j 3hmf 3iu5 3iu6 3k2j 3ljw 3mb4 3tlp 4q0n 4q0o 4y03 5fh6 5fh7 5fh8 5hrv 5hrw 5hrx 5ii1 5ii2 5iid

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