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(-) Description

Title :  THE DVL2 PDZ DOMAIN IN COMPLEX WITH THE N1 INHIBITORY PEPTIDE
 
Authors :  B. A. Appleton, C. Wiesmann
Date :  23 Feb 08  (Deposition) - 03 Mar 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pdz Domain, Phage Derived High Affinity Ligand, Cytoplasm, Developmental Protein, Phosphoprotein, Wnt Signaling Pathway, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhang, B. A. Appleton, C. Wiesmann, T. Lau, M. Costa, R. N. Hannoush, S. S. Sidhu
Inhibition Of Wnt Signaling By Dishevelled Pdz Peptides
Nat. Chem. Biol. V. 5 217 2009
PubMed-ID: 19252499  |  Reference-DOI: 10.1038/NCHEMBIO.152
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DISHEVELLED-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN (UNP RESIDUES 264-354)
    GeneDVL2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL- 2, DSH HOMOLOG 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:298 , ASP A:360 , GLY A:362 , HOH B:1193BINDING SITE FOR RESIDUE EDO A2002
2AC2SOFTWARESER B:298 , ASP B:360 , GLY B:362 , TRP B:363 , HOH B:1193BINDING SITE FOR RESIDUE EDO B2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CBY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CBY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064708I282TDVL2_HUMANUnclassified  ---A/BI282T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_HUMAN267-339
 
  2A:267-339
B:267-339
2DEPPS50186 DEP domain profile.DVL2_HUMAN433-507  1A:361-366

(-) Exons   (6, 11)

Asymmetric/Biological Unit (6, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000000053401ENSE00001296084chr17:7137868-7137388481DVL2_HUMAN1-65650--
1.2ENST000000053402ENSE00001741150chr17:7134116-713404770DVL2_HUMAN65-88240--
1.3ENST000000053403ENSE00001282250chr17:7133749-7133604146DVL2_HUMAN89-137490--
1.4ENST000000053404ENSE00001282244chr17:7133474-7133365110DVL2_HUMAN137-174380--
1.5ENST000000053405ENSE00001143281chr17:7133262-7133127136DVL2_HUMAN174-219460--
1.6ENST000000053406ENSE00001282234chr17:7132997-713290791DVL2_HUMAN219-249310--
1.7ENST000000053407ENSE00001282226chr17:7132766-713269770DVL2_HUMAN250-273242A:261-273 (gaps)
B:264-273
15
10
1.8ENST000000053408ENSE00001767013chr17:7132593-7132454140DVL2_HUMAN273-319472A:273-319 (gaps)
B:273-319 (gaps)
47
47
1.9ENST000000053409ENSE00001783234chr17:7132364-713228877DVL2_HUMAN320-345262A:320-345
B:320-345
26
26
1.10ENST0000000534010ENSE00001282202chr17:7131363-713129668DVL2_HUMAN345-368242A:345-353
B:345-354
9
10
1.11ENST0000000534011ENSE00001282195chr17:7131102-7130974129DVL2_HUMAN368-411442A:354-360
B:357-367 (gaps)
7
12
1.12ENST0000000534012ENSE00001282187chr17:7130854-7130723132DVL2_HUMAN411-455450--
1.13ENST0000000534013ENSE00001282182chr17:7130588-7130409180DVL2_HUMAN455-515611A:361-367
-
7
-
1.14ENST0000000534014ENSE00000887269chr17:7129958-7129740219DVL2_HUMAN515-588740--
1.15ENST0000000534015ENSE00001061609chr17:7129632-7128660973DVL2_HUMAN588-7361490--

(-) Sequences/Alignments

Asymmetric/Biological 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:101
 aligned with DVL2_HUMAN | O14641 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:211
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468 
           DVL2_HUMAN   259 STMSLNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLRDIVHKPGPIVLTVAKCWDPSPQAYFTLPRNEPIQPIDPAAWVSHSAALTGTFPAYPGSSSMSTITSGSSLPDGCEGRGLSVHTDMASVTKAMAAPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHHVEGF 469
               SCOP domains d3c  bya_ A: Segment polari      ty protein dishevelled homolog Dvl-2                                                                                                                                               SCOP domains
               CATH domains 3cb  yA00 A:261-367  [code=      2.30.42.10, no name defined]                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--.eeeeee.........eeeee.------..eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhhh....eeeeee.--------------------------------------------------hhh.eee----------------------------------------------------eee.... Sec.struct. author
                 SAPs(SNPs) -----------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: A:267-339 UniProt: 267-339                                     ---------------------------------------------------------------------------------------------DEP  PDB: A:361-366 UniProt: 433-507  PROSITE
           Transcript 1 (1) Exon 1.7       -----------------------------------------------------------------------Exon 1.10  PDB: A:345-35------------------------------------------Exon 1.12  PDB: - UniProt: 411-455           -------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.8  PDB: A:273-319 (gaps)                Exon 1.9  PDB: A:320-345  ----------------------Exon 1.11  PDB: A:354-360 UniProt: 368-411  -------------------------------------------Exon 1.13       Transcript 1 (2)
                 3cby A 261 SHM--NIITVTLNMEKYNFLGISIVGQ------GGIYIGSIMKGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLRDIVHKPGPIVLTVAK--------------------------------------------------SGGGWKD----------------------------------------------------YGWIDGK 367
                              |  | 268       278      |  -   |   298       308       318       328       338       348    |    -         -         -         -         -     | 358 |       -         -         -         -         -    |  366 
                              |  |                  285    292                                                          353                                                354   360                                                  361      
                            263  |                                                                                                                                                                                                             
                               264                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with DVL2_HUMAN | O14641 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:126
                                   273       283       293       303       313       323       333       343       353       363       373       383      
           DVL2_HUMAN   264 NIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLRDIVHKPGPIVLTVAKCWDPSPQAYFTLPRNEPIQPIDPAAWVSHSAALTGT 389
               SCOP domains d3cbyb_ B: Segment pola    rity protein dishevelled homolog Dvl-2                                                              SCOP domains
               CATH domains 3cbyB00 B:264-367  [cod    e=2.30.42.10, no name defined]                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.........eeeeee.----..eeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhhh....eeeeee..-----------------------..eee-ee.... Sec.struct. author
                 SAPs(SNPs) ------------------T----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: B:267-339 UniProt: 267-339                                     -------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  -----------------------------------------------------------------------Exon 1.10  PDB: B:345-35--------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.8  PDB: B:273-319 (gaps)                Exon 1.9  PDB: B:320-345  ----------------------Exon 1.11 [INCOMPLETE] Transcript 1 (2)
                 3cby B 264 NIITVTLNMEKYNFLGISIVGQS----DGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLRDIVHKPGPIVLTVAKS-----------------------GWKDY-GWIDGK 367
                                   273       283  |    293       303       313       323       333       343       353|        -         -    |   |-|     
                                                286  291                                                            354                     357 361 |     
                                                                                                                                                  362     

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CBY)

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DVL2_HUMAN | O14641)
molecular function
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0005109    frizzled binding    Interacting selectively and non-covalently with the frizzled (fz) receptor.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
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:0060071    Wnt signaling pathway, planar cell polarity pathway    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
    GO:1904886    beta-catenin destruction complex disassembly    The disaggregation of a beta-catenin destruction complex into its constituent components.
    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:0044340    canonical Wnt signaling pathway involved in regulation of cell proliferation    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 that contributes to modulating the rate or frequency of cell proliferation.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0090103    cochlea morphogenesis    The process in which the cochlea is generated and organized.
    GO:0022007    convergent extension involved in neural plate elongation    The process of directed cell movement in the neural plate resulting in tissue elongation via intercalation of adjacent cells in an epithelial sheet at the midline, leading to narrowing and lengthening of the neural plate.
    GO:0060029    convergent extension involved in organogenesis    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contribution to the shaping of an organ.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0035329    hippo signaling    The series of molecular signals mediated by the serine/threonine kinase Hippo or one of its orthologs. In Drosophila, Hippo in complex with the scaffold protein Salvador (Sav), phosphorylates and activates Warts (Wts), which in turn phosphorylates and inactivates the Yorkie (Yki) transcriptional activator. The core fly components hippo, sav, wts and mats are conserved in mammals as STK4/3 (MST1/2), SAV1/WW45, LATS1/2 and MOB1.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, 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.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0035567    non-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 effectors other than beta-catenin.
    GO:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0090179    planar cell polarity pathway involved in neural tube closure    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors that modulates the establishment of planar polarity contributing to neural tube closure.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043507    positive regulation of JUN kinase activity    Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, 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.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0061098    positive regulation of protein tyrosine kinase activity    Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0007379    segment specification    The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes.
    GO:0035282    segmentation    The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0045334    clathrin-coated endocytic vesicle    A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DVL2_HUMAN | O146412rey 3cbx 3cbz 3cc0 4wip 5lnp 5suy 5suz

(-) Related Entries Specified in the PDB File

3cbx 3cbz 3cc0