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(-) Description

Title :  STRUCTURE OF BRDT BROMODOMAIN 2 BOUND TO AN ACETYLATED HISTONE H3 PEPTIDE
 
Authors :  J. Moriniere, S. Rousseaux, U. Steuerwald, M. Soler-Lopez, S. Curtet, A. -L. Vitte, J. Govin, J. Gaucher, K. Sadoul, D. J. Hart, J. Krijgsveld, S. Khochbin, C. W. Mueller, C. Petosa
Date :  02 Aug 09  (Deposition) - 22 Sep 09  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Keywords :  Transcription Peptide Complex, Transcription Regulation, Acetyllysine Brdt, Nucleus, Coiled Coil, Chromosomal Protein, Nucleosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Moriniere, S. Rousseaux, U. Steuerwald, M. Soler-Lopez, S. Curtet, A. -L. Vitte, J. Govin, J. Gaucher, K. Sadoul, D. J. Hart, J. Krijgsveld, S. Khochbin, C. W. Mueller, C. Petosa
Cooperative Binding Of Two Acetylation Marks On A Histone Tail By A Single Bromodomain.
Nature V. 461 664 2009
PubMed-ID: 19794495  |  Reference-DOI: 10.1038/NATURE08397

(-) Compounds

Molecule 1 - BROMODOMAIN TESTIS-SPECIFIC PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentBROMODOMAIN 2, RESIDUES 257-382
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRING3-LIKE PROTEIN, BROMODOMAIN-CONTAINING FEMALE STERILE HOMEOTIC-LIKE PROTEIN
 
Molecule 2 - HISTONE H3
    ChainsP, Q
    FragmentACETYLATED H3 PEPTIDE, RESIDUES 15-24
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABPQ
Biological Unit 1 (1x)A P 
Biological Unit 2 (1x) B Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2WP1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WP1)

(-) PROSITE Motifs  (3, 5)

Asymmetric Unit (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H31_MOUSE15-21  1Q:14-20
2BROMODOMAIN_2PS50014 Bromodomain profile.BRDT_MOUSE43-115
286-358
 
  2-
A:286-358
B:286-358
3BROMODOMAIN_1PS00633 Bromodomain signature.BRDT_MOUSE48-107
291-350
 
  2-
A:291-350
B:291-350
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H31_MOUSE15-21  0-
2BROMODOMAIN_2PS50014 Bromodomain profile.BRDT_MOUSE43-115
286-358
 
  1-
A:286-358
-
3BROMODOMAIN_1PS00633 Bromodomain signature.BRDT_MOUSE48-107
291-350
 
  1-
A:291-350
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H31_MOUSE15-21  1Q:14-20
2BROMODOMAIN_2PS50014 Bromodomain profile.BRDT_MOUSE43-115
286-358
 
  1-
-
B:286-358
3BROMODOMAIN_1PS00633 Bromodomain signature.BRDT_MOUSE48-107
291-350
 
  1-
-
B:291-350

(-) Exons   (0, 0)

(no "Exon" information available for 2WP1)

(-) 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:124
 aligned with BRDT_MOUSE | Q91Y44 from UniProtKB/Swiss-Prot  Length:956

    Alignment length:124
                                   268       278       288       298       308       318       328       338       348       358       368       378    
           BRDT_MOUSE   259 QHKVLKTVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDEPIES 382
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------BROMODOMAIN_2  PDB: A:286-358 UniProt: 286-358                           ------------------------ PROSITE (1)
                PROSITE (2) --------------------------------BROMODOMAIN_1  PDB: A:291-350 UniProt: 291-350              -------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wp1 A 259 QHKVLKTVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDEPIES 382
                                   268       278       288       298       308       318       328       338       348       358       368       378    

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with BRDT_MOUSE | Q91Y44 from UniProtKB/Swiss-Prot  Length:956

    Alignment length:113
                                   274       284       294       304       314       324       334       344       354       364       374   
           BRDT_MOUSE   265 TVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPD 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BROMODOMAIN_2  PDB: B:286-358 UniProt: 286-358                           ------------------- PROSITE (1)
                PROSITE (2) --------------------------BROMODOMAIN_1  PDB: B:291-350 UniProt: 291-350              --------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2wp1 B 265 TVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPD 377
                                   274       284       294       304       314       324       334       344       354       364       374   

Chain P from PDB  Type:PROTEIN  Length:8
 aligned with B9EI85_MOUSE | B9EI85 from UniProtKB/TrEMBL  Length:136

    Alignment length:8
         B9EI85_MOUSE    16 APRKQLAT  23
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2wp1 P  15 APRkQLAT  22
                               |    
                               |    
                              18-ALY

Chain P from PDB  Type:PROTEIN  Length:8
 aligned with H31_MOUSE | P68433 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_MOUSE    16 APRKQLAT  23
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE HISTON-- PROSITE
                 Transcript -------- Transcript
                 2wp1 P  15 APRkQLAT  22
                               |    
                              18-ALY

Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with B9EI85_MOUSE | B9EI85 from UniProtKB/TrEMBL  Length:136

    Alignment length:10
                                    24
         B9EI85_MOUSE    15 KAPRKQLATK  24
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2wp1 Q  14 KAPRkQLATK  23
                                |   23
                               18-ALY 

Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with H31_MOUSE | P68433 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    24
            H31_MOUSE    15 KAPRKQLATK  24
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE HISTONE--- PROSITE
                 Transcript ---------- Transcript
                 2wp1 Q  14 KAPRkQLATK  23
                                |   23
                               18-ALY 

   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 2WP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WP1)

(-) Gene Ontology  (37, 45)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BRDT_MOUSE | Q91Y44)
molecular function
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0001207    histone displacement    The removal of histones, including histone dimers, from nucleosomes within chromatin.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0007141    male meiosis I    A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline.
    GO:0007140    male meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0051039    positive regulation of transcription involved in meiotic cell cycle    Any process that activates or increases the frequency, rate or extent of transcription as part of a meiotic cell cycle.
    GO:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain P,Q   (B9EI85_MOUSE | B9EI85)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain P,Q   (H31_MOUSE | P68433)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0032776    DNA methylation on cytosine    The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0060968    regulation of gene silencing    Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRDT_MOUSE | Q91Y442wp2
        H31_MOUSE | P684331cs9 1ct6 1guw 1q3l 1u35 2v83 2w5z 2xl3 4ezh 5b1l 5b1m 5ix1 5ix2

(-) Related Entries Specified in the PDB File

2wp2 STRUCTURE OF BRDT BROMODOMAIN BD1 BOUND TO AN ACETYLATED HISTONE H4 PEPTIDE.