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(-) Description

Title :  N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B PEPTIDE
 
Authors :  G. Moncalian, N. Cardenes, Y. L. Deribe, M. Spinola-Amilibia, I. Dikic
Date :  28 Sep 06  (Deposition) - 11 Oct 06  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Metal-Binding, Immune Response, Sh3, Ligase, Sh2 Domain, Sh3 Domain, Zinc-Finger, Sh3- Binding, Ubl Conjugation Pathway, Cytoskeletal Rearrangements, Phosphorylation, Adaptor Protein, Egfr Downregulation, Cd2 Associated Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Moncalian, N. Cardenes, Y. L. Deribe, M. Spinola-Amilibia, I. Dikic, J. Bravo
Atypical Polyproline Recognition By The Cms N- Terminal Sh3 Domain.
J. Biol. Chem. V. 281 38845 2006
PubMed-ID: 17020880  |  Reference-DOI: 10.1074/JBC.M606411200

(-) Compounds

Molecule 1 - CD2-ASSOCIATED PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainROSETTA (DE3) PLYS
    Expression System Taxid562
    FragmentSH3, RESIDUES 1-62
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsN-TERMINAL SH3 DOMAIN (SH3A) OF CD2- ASSOCIATED PROTEIN (CD2AP)OR CAS LIGAND WITH MULTIPLE SRC HOMOLOGY 3 DOMAINS (CMS)
    SynonymCAS LIGAND WITH MULTIPLE SH3 DOMAINS, ADAPTER PROTEIN CMS
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE CBL-B
    ChainsC
    EC Number6.3.2.-
    EngineeredYES
    FragmentPEPTIDE, RESIDUES 902-912
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsA.A. 902 TO 912 FROM CAS-BR-M (MURINE) ECTROPIC RETROVIRAL TRANSFORMING SEQUENCE B (CBL-B)
    SynonymCAS-BR-M MURINE ECTROPIC RETROVIRAL TRANSFORMING SEQUENCE B, CBL-B, SIGNAL TRANSDUCTION PROTEIN CBL-B, SH3-BINDING PROTEIN CBL-B, CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B, RING FINGER PROTEIN 56
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2J6F)

(-) Sites  (0, 0)

(no "Site" information available for 2J6F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J6F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J6F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J6F)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000002641222dENSE00001340691chr3:105587887-105587580308CBLB_HUMAN-00--
1.3ENST000002641223ENSE00002109512chr3:105586435-105586254182CBLB_HUMAN1-56560--
1.4ENST000002641224ENSE00002192869chr3:105572508-105572258251CBLB_HUMAN57-140840--
1.5ENST000002641225ENSE00001686511chr3:105495386-105495240147CBLB_HUMAN140-189500--
1.6ENST000002641226ENSE00001628201chr3:105470462-105470306157CBLB_HUMAN189-241530--
1.7ENST000002641227ENSE00001692048chr3:105464882-105464761122CBLB_HUMAN242-282410--
1.8ENST000002641228ENSE00001696958chr3:105459475-105459338138CBLB_HUMAN282-328470--
1.9ENST000002641229ENSE00001616258chr3:105456102-10545601588CBLB_HUMAN328-357300--
1.10ENST0000026412210ENSE00001694160chr3:105452984-105452853132CBLB_HUMAN358-401440--
1.11ENST0000026412211ENSE00001654827chr3:105439094-105438891204CBLB_HUMAN402-469680--
1.12ENST0000026412212ENSE00001767402chr3:105423017-105422832186CBLB_HUMAN470-531620--
1.13aENST0000026412213aENSE00001607504chr3:105421303-105420938366CBLB_HUMAN532-6531220--
1.14ENST0000026412214ENSE00000774846chr3:105412432-10541233895CBLB_HUMAN654-685320--
1.15ENST0000026412215ENSE00000774845chr3:105404310-105404164147CBLB_HUMAN685-734500--
1.16bENST0000026412216bENSE00000774844chr3:105400662-10540056895CBLB_HUMAN734-766330--
1.16dENST0000026412216dENSE00000774843chr3:105400454-105400323132CBLB_HUMAN766-810450--
1.17ENST0000026412217ENSE00000774842chr3:105397415-105397275141CBLB_HUMAN810-857480--
1.18bENST0000026412218bENSE00000774841chr3:105389196-105389077120CBLB_HUMAN857-897410--
1.19dENST0000026412219dENSE00001755904chr3:105378073-1053743053769CBLB_HUMAN897-982861C:905-9128

2.1ENST000003593141ENSE00001516297chr6:47445525-47445984460CD2AP_HUMAN1-221A:2-21
2.2ENST000003593142ENSE00000755720chr6:47471016-47471176161CD2AP_HUMAN2-55541A:2-5554
2.3aENST000003593143aENSE00000619362chr6:47501338-47501491154CD2AP_HUMAN56-107521A:56-594
2.4aENST000003593144aENSE00001139103chr6:47512342-47512442101CD2AP_HUMAN107-140340--
2.5ENST000003593145ENSE00001139093chr6:47522382-47522502121CD2AP_HUMAN141-181410--
2.6ENST000003593146ENSE00001139085chr6:47541800-47541987188CD2AP_HUMAN181-243630--
2.7bENST000003593147bENSE00001139077chr6:47544260-4754433879CD2AP_HUMAN244-270270--
2.8ENST000003593148ENSE00002190760chr6:47544745-4754483995CD2AP_HUMAN270-301320--
2.9aENST000003593149aENSE00001139061chr6:47547121-47547225105CD2AP_HUMAN302-336350--
2.10ENST0000035931410ENSE00002145560chr6:47548600-4754863637CD2AP_HUMAN337-349130--
2.11aENST0000035931411aENSE00001139049chr6:47549739-4754980163CD2AP_HUMAN349-370220--
2.12ENST0000035931412ENSE00001139043chr6:47563597-47563762166CD2AP_HUMAN370-425560--
2.13ENST0000035931413ENSE00001139036chr6:47567037-47567179143CD2AP_HUMAN425-473490--
2.14ENST0000035931414ENSE00001139029chr6:47573901-47574013113CD2AP_HUMAN473-510380--
2.15bENST0000035931415bENSE00001139023chr6:47575663-47575764102CD2AP_HUMAN511-544340--
2.16aENST0000035931416aENSE00001139019chr6:47576859-47577040182CD2AP_HUMAN545-605610--
2.17ENST0000035931417ENSE00001176400chr6:47580209-4758027264CD2AP_HUMAN605-626220--
2.18ENST0000035931418ENSE00001454693chr6:47591922-475949993078CD2AP_HUMAN627-639130--

(-) 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:58
 aligned with CD2AP_HUMAN | Q9Y5K6 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:58
                                    11        21        31        41        51        
          CD2AP_HUMAN     2 VDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKR  59
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains 2j6fA00 A:2-59 SH3 Domains                                 CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................eeeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
           Transcript 2 (1) 2-----------------------------------------------------2.3a Transcript 2 (1)
           Transcript 2 (2) Exon 2.2  PDB: A:2-55 UniProt: 2-55                   ---- Transcript 2 (2)
                 2j6f A   2 VDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKR  59
                                    11        21        31        41        51        

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:8
           CBLB_HUMAN   905 PPKPRPRR 912
               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 1 1.19d    Transcript 1
                 2j6f C 905 PPKPRPRR 912

   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 2J6F)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J6F)

(-) Gene Ontology  (54, 58)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD2AP_HUMAN | Q9Y5K6)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0045296    cadherin binding    Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005172    vascular endothelial growth factor receptor binding    Interacting selectively and non-covalently with any vascular endothelial growth factor receptor.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0032911    negative regulation of transforming growth factor beta1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of transforming growth factor-beta1.
    GO:1900182    positive regulation of protein localization to nucleus    Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:2000249    regulation of actin cytoskeleton reorganization    Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0048259    regulation of receptor-mediated endocytosis    Any process that modulates the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0006930    substrate-dependent cell migration, cell extension    The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    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:0031941    filamentous actin    A two-stranded helical polymer of the protein actin.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.
    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.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain C   (CBLB_HUMAN | Q13191)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    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: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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0023051    regulation of signaling    Any process that modulates the frequency, rate or extent of a signaling process.
    GO:0009629    response to gravity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus.
    GO:0009725    response to hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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.
    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
        CBLB_HUMAN | Q131912ak5 2bz8 2do6 2jnh 2ldr 2ooa 2oob 3pfv 3vgo 3zni
        CD2AP_HUMAN | Q9Y5K62fei 2j6k 2j6o 2j7i 3aa6 3lk4 3u23 4wci 4x1v

(-) Related Entries Specified in the PDB File

2j6k N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG)
2j6o ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETEROTRIMER
2j7i ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN.CMS:CD2 HETERODIMER