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(-) Description

Title :  N-TERMINAL SH3 DOMAIN OF CIN85 BOUND TO CBL-B PEPTIDE
 
Authors :  N. Cardenes, G. Moncalian, J. Bravo
Date :  12 Aug 05  (Deposition) - 05 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Sh3 Domain, Cin85 Adaptor Protein, Cbl Ubiquitin Ligase, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Jozic, N. Cardenes, Y. Lissanu-Deribe, G. Moncalian, D. Hoeller, Y. Groemping, I. Dikic, K. Rittinger, J. Bravo
Cbl Promotes Clustering Of Endocytic Adaptor Proteins
Nat. Struct. Mol. Biol. V. 12 972 2005
PubMed-ID: 16228008  |  Reference-DOI: 10.1038/NSMB1000

(-) Compounds

Molecule 1 - SH3-DOMAIN KINASE BINDING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET29B
    Expression System StrainROSETTA(DE3)PLYS
    Expression System Taxid562
    FragmentN-TERMINAL SH3 DOMAIN RESIDUES 1-58
    OrganBRAIN, KIDNEY, HEART, PLACENTA, LUNG, LIVER, SKELETAL MUSCLE, PANCREAS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCBL-INTERACTING PROTEIN OF 85KDA, HUMAN SRC-FAMILY KINASE BINDING PROTEIN 1, HSB-1, CD2 BINDING PROTEIN 3, CD2BP3, CIN85
 
Molecule 2 - SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B
    ChainsC
    FragmentPOLYPROLINE RICH REGION RESIDUES 902-912
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , VAL A:53 , HOH A:2004 , HOH A:2033 , HOH A:2038BINDING SITE FOR RESIDUE NA A1058
2AC2SOFTWAREASP B:50 , VAL B:53 , HOH B:2015 , HOH B:2030BINDING SITE FOR RESIDUE NA B1059

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BZ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BZ8)

(-) Exons   (4, 7)

Asymmetric/Biological Unit (4, 7)
 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:902-91211

2.1aENST000003978211aENSE00002155133X:19905719-19905425295SH3K1_HUMAN1-222A:2-2
B:2-2
1
1
2.2ENST000003978212ENSE00001789519X:19854400-19854243158SH3K1_HUMAN2-54532A:2-54
B:2-54
53
53
2.5aENST000003978215aENSE00001709790X:19764559-19764436124SH3K1_HUMAN55-96422A:55-58
B:55-58
4
4
2.8ENST000003978218ENSE00001200119X:19725102-19724999104SH3K1_HUMAN96-130350--
2.9aENST000003978219aENSE00001200111X:19713859-19713730130SH3K1_HUMAN131-174440--
2.12bENST0000039782112bENSE00002170582X:19702146-19701941206SH3K1_HUMAN174-242690--
2.15bENST0000039782115bENSE00001752859X:19663593-1966351876SH3K1_HUMAN243-268260--
2.16ENST0000039782116ENSE00001789134X:19650076-1964998295SH3K1_HUMAN268-299320--
2.17ENST0000039782117ENSE00001667936X:19626163-19626056108SH3K1_HUMAN300-335360--
2.19ENST0000039782119ENSE00001798573X:19613118-1961306752SH3K1_HUMAN336-353180--
2.20bENST0000039782120bENSE00001780198X:19610265-1961018581SH3K1_HUMAN353-380280--
2.21bENST0000039782121bENSE00001781910X:19606920-19606761160SH3K1_HUMAN380-433540--
2.22ENST0000039782122ENSE00001696322X:19587306-1958722186SH3K1_HUMAN433-462300--
2.23ENST0000039782123ENSE00001670343X:19568201-19568092110SH3K1_HUMAN462-498370--
2.24ENST0000039782124ENSE00001757635X:19564168-19564040129SH3K1_HUMAN499-541430--
2.25ENST0000039782125ENSE00001659172X:19560311-19560043269SH3K1_HUMAN542-631900--
2.26ENST0000039782126ENSE00001632685X:19555898-1955583564SH3K1_HUMAN631-652220--
2.27eENST0000039782127eENSE00001938509X:19554576-195520932484SH3K1_HUMAN653-665130--

(-) 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:57
 aligned with SH3K1_HUMAN | Q96B97 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:57
                                    11        21        31        41        51       
          SH3K1_HUMAN     2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains 2bz8A00 A:2-58 SH3 Domains                                CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................eeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
           Transcript 2 (1) 2----------------------------------------------------2.5a Transcript 2 (1)
           Transcript 2 (2) Exon 2.2  PDB: A:2-54 UniProt: 2-54                  ---- Transcript 2 (2)
                 2bz8 A   2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
                                    11        21        31        41        51       

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with SH3K1_HUMAN | Q96B97 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:57
                                    11        21        31        41        51       
          SH3K1_HUMAN     2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains 2bz8B00 B:2-58 SH3 Domains                                CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................eeeeee.....eeeee....eeeee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
           Transcript 2 (1) 2----------------------------------------------------2.5a Transcript 2 (1)
           Transcript 2 (2) Exon 2.2  PDB: B:2-54 UniProt: 2-54                  ---- Transcript 2 (2)
                 2bz8 B   2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
                                    11        21        31        41        51       

Chain C from PDB  Type:PROTEIN  Length:11
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:11
                                   911 
           CBLB_HUMAN   902 PARPPKPRPRR 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 Exon 1.19d  Transcript 1
                 2bz8 C 902 PARPPKPRPRR 912
                                   911 

   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 2BZ8)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BZ8)

(-) Gene Ontology  (41, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SH3K1_HUMAN | Q96B97)
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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 2do6 2j6f 2jnh 2ldr 2ooa 2oob 3pfv 3vgo 3zni
        SH3K1_HUMAN | Q96B972k6d 2k9g 2n64 2o2o 2ydl 5abs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BZ8)