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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIFTH BROMODOMAIN OF HUMAN POLY-BROMODOMAIN CONTAINING PROTEIN 1 (PB1) IN COMPLEX WITH A HYDROXYPHENYL-PROPENONE LIGAND
 
Authors :  P. Filippakopoulos, S. Picaud, I. Felletar, S. Martin, O. Monteiro, O. A. Chaikuad, W. Yue, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. B S. Knapp, Structural Genomics Consortium (Sgc)
Date :  02 Apr 14  (Deposition) - 07 May 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Keywords :  Pb1, Polybromo 1 Isoform 1, Baf180, Polybromo-1D, Pbrm1, Brg1- Associated Factor 180, Bromodomain, Chromatin Regulator, Dna- Binding, Nucleus, Transcription, Transcription Regulation, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Filippakopoulos, S. Picaud, I. Felletar, S. Martin, O. Monteiro, O. Fedorov, A. Chaikuad, W. Yue, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Fifth Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) In Complex With A Hydroxyphenyl-Propenone Ligand
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN POLYBROMO-1
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 645-766
    Gene: BAF180, PB1, PBRM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPB1, BRG1-ASSOCIATED FACTOR 180, BAF180, POLYBROMO-1D

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
12XD8Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 7 (2, 3)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 8 (2, 2)
No.NameCountTypeFull Name
12XD1Ligand/Ion(2E)-1-(2-HYDROXYPHENYL)-3-(2,4,5,7-TETRAHYDRO-6H-PYRAZOLO[3,4-C]PYRIDIN-6-YL)PROP-2-EN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:700 , ASN A:701 , CYS A:704 , LEU A:718 , HIS A:721 , ARG E:658 , TYR E:665 , HOH E:921BINDING SITE FOR RESIDUE EDO A 801
02AC2SOFTWAREILE A:651 , PHE A:652 , PRO A:656 , GLU A:660 , LEU A:661 , TYR A:664 , MET A:672 , ALA A:703 , ASN A:707 , ILE A:713 , HOH A:919BINDING SITE FOR RESIDUE 2XD A 802
03AC3SOFTWAREILE B:651 , PHE B:652 , LEU B:655 , TYR B:664 , MET B:672 , ALA B:703 , ASN B:707 , HOH B:909 , HOH B:923 , 2XD D:802BINDING SITE FOR RESIDUE 2XD B 801
04AC4SOFTWAREARG C:646 , LYS C:715 , ASP C:716 , HOH C:948 , GLU G:660BINDING SITE FOR RESIDUE EDO C 801
05AC5SOFTWAREILE C:651 , PHE C:652 , LEU C:655 , PRO C:656 , TYR C:664 , MET C:672 , ALA C:703 , ASN C:707 , ILE C:713 , HOH C:931BINDING SITE FOR RESIDUE 2XD C 802
06AC6SOFTWAREPHE D:700 , ASN D:701 , CYS D:704 , LEU D:718 , HIS D:721BINDING SITE FOR RESIDUE EDO D 801
07AC7SOFTWARE2XD B:801 , ILE D:651 , PHE D:652 , LEU D:655 , PRO D:656 , GLU D:660 , TYR D:664 , MET D:672 , ALA D:703 , ASN D:707 , ILE D:713 , HOH D:917 , HOH D:952BINDING SITE FOR RESIDUE 2XD D 802
08AC8SOFTWAREARG A:658 , TYR A:665 , PHE E:700 , ASN E:701 , CYS E:704 , HIS E:721 , HOH E:941BINDING SITE FOR RESIDUE EDO E 801
09AC9SOFTWAREPRO E:656 , SER E:657 , GLU E:660 , GLU H:710 , LEU H:712 , LYS H:715BINDING SITE FOR RESIDUE EDO E 802
10BC1SOFTWAREILE E:651 , PHE E:652 , PRO E:656 , GLU E:660 , TYR E:664 , MET E:672 , ALA E:703 , ASN E:707 , ILE E:713 , HOH E:913 , 2XD H:802BINDING SITE FOR RESIDUE 2XD E 803
11BC2SOFTWAREHOH A:913 , ILE F:651 , LEU F:712 , ASP F:716 , HOH F:906 , HOH F:931BINDING SITE FOR RESIDUE EDO F 801
12BC3SOFTWAREILE A:651 , LEU A:712 , HOH A:911 , HOH A:917 , ILE F:651 , PHE F:652 , LEU F:655 , TYR F:664 , MET F:672 , ALA F:703 , ASN F:707BINDING SITE FOR RESIDUE 2XD F 802
13BC4SOFTWAREPHE G:700 , ASN G:701 , CYS G:704 , LEU G:718 , HIS G:721 , HOH G:938BINDING SITE FOR RESIDUE EDO G 801
14BC5SOFTWAREALA C:650 , ILE C:651 , HOH C:927 , ILE G:651 , ASP G:716 , HOH G:908BINDING SITE FOR RESIDUE EDO G 802
15BC6SOFTWAREHOH C:903 , ILE G:651 , PHE G:652 , LEU G:655 , TYR G:664 , MET G:672 , MET G:699 , ALA G:703 , ASN G:707 , ILE G:713 , HOH G:903BINDING SITE FOR RESIDUE 2XD G 803
16BC7SOFTWAREILE H:651 , ILE H:713 , ASP H:716 , HOH H:908 , HOH H:943 , HOH H:965BINDING SITE FOR RESIDUE EDO H 801
17BC8SOFTWAREILE E:651 , LEU E:712 , ILE E:713 , 2XD E:803 , HOH E:934 , ILE H:651 , PHE H:652 , LEU H:655 , TYR H:664 , MET H:672 , ALA H:703 , ASN H:707 , HOH H:915BINDING SITE FOR RESIDUE 2XD H 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q0N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q0N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q0N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q0N)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q0N)

(-) 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:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n A 620 SKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE 732
                                   629       639       649       659       669       679       689       699       709       719       729   


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.......hhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n 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........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n C 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730 


Chain D from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n D 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE 732
                                   630       640       650       660       670       680       690       700       710       720       730  


Chain E from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n E 620 SKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE 732
                                   629       639       649       659       669       679       689       699       709       719       729   


Chain F from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4q0n F 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE 732
                                   630       640       650       660       670       680       690       700       710       720       730  


Chain G from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               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
                 4q0n G 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE 732
                                   630       640       650       660       670       680       690       700       710       720       730  


Chain H 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
                 4q0n H 621 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 731
                                   630       640       650       660       670       680       690       700       710       720       730
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  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 4Q0N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q0N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q0N)

(-) Gene Ontology  (11, 11)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PB1_HUMAN | Q86U86: 2ktb 3g0j 3hmf 3iu5 3iu6 3k2j 3ljw 3mb4 3tlp 4q0o 4y03 5e7d 5fh6 5fh7 5fh8 5hrv 5hrw 5hrx 5ii1 5ii2 5iid

(-) Related Entries Specified in the PDB File

4q0o