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(-) Description

Title :  DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX
 
Authors :  M. Fiedler, M. J. Sanchez-Barrena, M. Nekrasov, J. Mieszczanek, V. Rybin, J. Muller, P. Evans, M. Bienz
Date :  27 Feb 08  (Deposition) - 17 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,P,R
Biol. Unit 1:  A,B,P  (1x)
Biol. Unit 2:  C,D,R  (1x)
Keywords :  Gene Regulation, Wnt Signaling Pathway, Wnt Signaling Complex, Chromosomal Rearrangement, Signaling Protein, Bcl9 Hd1 Domain, Hpygo1 Phd Domain, Proto-Oncogene, Phosphoprotein, Histone H3K4Me2, Zinc, Nucleus, Zinc-Finger, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Fiedler, M. J. Sanchez-Barrena, M. Nekrasov, J. Mieszczanek, V. Rybin, J. Muller, P. Evans, M. Bienz
Decoding Of Methylated Histone H3 Tail By The Pygo- Bcl9 Wnt Signaling Complex.
Mol. Cell V. 30 507 2008
PubMed-ID: 18498752  |  Reference-DOI: 10.1016/J.MOLCEL.2008.03.011

(-) Compounds

Molecule 1 - PYGOPUS HOMOLOG 1
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantCODONPLUS(DE3)-RIL
    Expression System VectorBI-CISTRONIC EXPRESSION VECTOR
    FragmentPHD DOMAIN, RESIDUES 340-398
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHPYGO1
 
Molecule 2 - B-CELL CLL/LYMPHOMA 9 PROTEIN
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantCODONPLUS(DE3)-RIL
    Expression System VectorBI-CISTRONIC EXPRESSION VECTOR
    FragmentHD1 DOMAIN, RESIDUES 177-205
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymB-CELL LYMPHOMA 9 PROTEIN, BCL-9, PROTEIN LEGLESS HOMOLOG, BCL9
 
Molecule 3 - HISTONE H3 TAIL
    ChainsP, R
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other Details9-MER H3K4ME2, DIMETHYLATION AT LYS K4
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDPR
Biological Unit 1 (1x)AB  P 
Biological Unit 2 (1x)  CD R

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY2Mod. Amino AcidN-DIMETHYL-LYSINE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:354 , HIS A:368 , HOH A:2076 , HOH A:2077 , HOH A:2078 , GLY C:336 , ASN C:348BINDING SITE FOR RESIDUE GOL A1399
2AC2SOFTWARECYS C:343 , CYS C:346 , HIS C:368 , CYS C:371BINDING SITE FOR RESIDUE ZN C1398
3AC3SOFTWARECYS C:359 , CYS C:363 , CYS C:392 , CYS C:395BINDING SITE FOR RESIDUE ZN C1399
4AC4SOFTWARECYS A:343 , CYS A:346 , HIS A:368 , CYS A:371BINDING SITE FOR RESIDUE ZN A1400
5AC5SOFTWARECYS A:359 , CYS A:363 , CYS A:392 , CYS A:395BINDING SITE FOR RESIDUE ZN A1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.PYGO1_HUMAN340-398
 
  2A:340-398
C:340-397
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.PYGO1_HUMAN343-395
 
  2A:343-395
C:343-395
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.PYGO1_HUMAN340-398
 
  1A:340-398
-
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.PYGO1_HUMAN343-395
 
  1A:343-395
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.PYGO1_HUMAN340-398
 
  1-
C:340-397
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.PYGO1_HUMAN343-395
 
  1-
C:343-395

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002347391ENSE00001344656chr1:147013182-147013444263BCL9_HUMAN-00--
1.3ENST000002347393ENSE00001344647chr1:147076570-147076704135BCL9_HUMAN-00--
1.4ENST000002347394ENSE00001344643chr1:147078577-14707865983BCL9_HUMAN-00--
1.5bENST000002347395bENSE00001156130chr1:147083377-147083688312BCL9_HUMAN1-18180--
1.6bENST000002347396bENSE00000824226chr1:147084682-147084998317BCL9_HUMAN18-1241070--
1.7ENST000002347397ENSE00000787540chr1:147086226-147086415190BCL9_HUMAN124-187642B:174-187
D:174-187
14
14
1.8ENST000002347398ENSE00000787541chr1:147087603-147087702100BCL9_HUMAN187-220342B:187-203
D:187-202
17
16
1.9ENST000002347399ENSE00000787543chr1:147090622-1470928632242BCL9_HUMAN221-9687480--
1.10ENST0000023473910ENSE00000903093chr1:147094072-147094332261BCL9_HUMAN968-1055880--
1.11ENST0000023473911ENSE00001156122chr1:147095643-1470980172375BCL9_HUMAN1055-14263720--

(-) 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:61
 aligned with PYGO1_HUMAN | Q9Y3Y4 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:61
                                   347       357       367       377       387       397 
          PYGO1_HUMAN   338 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMAD 398
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee.......eeehhhhh.hhhhhhhhhhh..eee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZF_PHD_2  PDB: A:340-398 UniProt: 340-398                   PROSITE (1)
                PROSITE (2) -----ZF_PHD_1  PDB: A:343-395 UniProt: 343-395            --- PROSITE (2)
                 Transcript ------------------------------------------------------------- Transcript
                 2vpe A 338 MAVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMAD 398
                                   347       357       367       377       387       397 

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with BCL9_HUMAN | O00512 from UniProtKB/Swiss-Prot  Length:1426

    Alignment length:30
                                   183       193       203
           BCL9_HUMAN   174 AKVVYVFSTEMANKAAEAVLKGQVETIVSF 203
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7      ---------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.8          Transcript 1 (2)
                 2vpe B 174 GAMVYVFSTEMANKAAEAVLKGQVETIVSF 203
                                   183       193       203

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with PYGO1_HUMAN | Q9Y3Y4 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:62
                                   345       355       365       375       385       395  
          PYGO1_HUMAN   336 SSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMA 397
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
           Pfam domains (1) ------PHD-2vpeC01 C:342-397                                    Pfam domains (1)
           Pfam domains (2) ------PHD-2vpeC02 C:342-397                                    Pfam domains (2)
         Sec.struct. author ....................eee.......eeehhhhh.hhhhhhhhhhh..eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ZF_PHD_2  PDB: C:340-397 UniProt: 340-398                  PROSITE (1)
                PROSITE (2) -------ZF_PHD_1  PDB: C:343-395 UniProt: 343-395            -- PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                 2vpe C 336 GAMAVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMA 397
                                   345       355       365       375       385       395  

Chain D from PDB  Type:PROTEIN  Length:29
 aligned with BCL9_HUMAN | O00512 from UniProtKB/Swiss-Prot  Length:1426

    Alignment length:29
                                   183       193         
           BCL9_HUMAN   174 AKVVYVFSTEMANKAAEAVLKGQVETIVS 202
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
           Transcript 1 (1) Exon 1.7      --------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.8         Transcript 1 (2)
                 2vpe D 174 GAMVYVFSTEMANKAAEAVLKGQVETIVS 202
                                   183       193         

Chain P from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2vpe P   1 ARTkQTA   7
                               |   
                               4-MLY

Chain R from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2vpe R   1 ARTkQTA   7
                               |   
                               4-MLY

   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 2VPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: PHD (44)
1aPHD-2vpeC01C:342-397
1bPHD-2vpeC02C:342-397

(-) Gene Ontology  (23, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (PYGO1_HUMAN | Q9Y3Y4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0034504    protein localization to nucleus    A process in which a protein transports or maintains the localization of another protein to the nucleus.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    GO:0007289    spermatid nucleus differentiation    The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 B,D   (BCL9_HUMAN | O00512)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    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:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0014908    myotube differentiation involved in skeletal muscle regeneration    The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. This process occurs as part of the process of skeletal muscle regeneration. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0017015    regulation of transforming growth factor beta receptor signaling pathway    Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005801    cis-Golgi network    The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BCL9_HUMAN | O005122gl7 2vp7 2vpb 2vpd 2vpg 3sl9
        PYGO1_HUMAN | Q9Y3Y42vp7 2vpb 2vpd 2vpg

(-) Related Entries Specified in the PDB File

2vp7 DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX
2vpb DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX
2vpd DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX
2vpg DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX