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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-CBL TKB DOMAIN IN COMPLEX WITH THE APS PTYR-618 PHOSPHOPEPTIDE
 
Authors :  J. Hu, S. R. Hubbard
Date :  15 Feb 05  (Deposition) - 08 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  X-Ray Crystallography; Phosphotyrosine; Adapter Protein, Ligase, Signaling Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Hu, S. R. Hubbard
Structural Characterization Of A Novel Cbl Phosphotyrosine Recognition Motif In The Aps Family Of Adapter Proteins
J. Biol. Chem. V. 280 18943 2005
PubMed-ID: 15737992  |  Reference-DOI: 10.1074/JBC.M414157200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CBL E3 UBIQUITIN PROTEIN LIGASE
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTYROSINE KINASE BINDING DOMAIN, RESIDUES 25-351
    GeneCBL, CBL2, RNF55
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSIGNAL TRANSDUCTION PROTEIN CBL
 
Molecule 2 - 13-MER FRAGMENT OF SH2 AND PH DOMAIN-CONTAINING ADAPTER PROTEIN APS
    ChainsB
    EngineeredYES
    FragmentPTYR-618 PHOSPHOPEPTIDE
    Other DetailsSEQUENCE APPEARS IN RATTUS NORVEGICUS, GENE APS
    SynonymAPS ADAPTER PROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:229 , THR A:231 , ASN A:233 , TYR A:235 , GLU A:240 , HOH A:382BINDING SITE FOR RESIDUE MG A 352

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YVH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:81 -Pro A:82
2Gln A:249 -Pro A:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071040K287RCBL_HUMANUnclassified  ---AK287R

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YVH)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000019351ENSRNOE00000319944chr12:21544434-21544670237SH2B2_RAT-00--
1.2ENSRNOT000000019352ENSRNOE00000013532chr12:21557200-21557933734SH2B2_RAT1-2362360--
1.3ENSRNOT000000019353ENSRNOE00000013533chr12:21562832-21562933102SH2B2_RAT237-270340--
1.4ENSRNOT000000019354ENSRNOE00000013534chr12:21564742-2156483392SH2B2_RAT271-301310--
1.5ENSRNOT000000019355ENSRNOE00000013542chr12:21565636-2156572792SH2B2_RAT301-332320--
1.6ENSRNOT000000019356ENSRNOE00000013543chr12:21565816-21565983168SH2B2_RAT332-388570--
1.7ENSRNOT000000019357ENSRNOE00000013544chr12:21567528-21567742215SH2B2_RAT388-459720--
1.8ENSRNOT000000019358ENSRNOE00000013538chr12:21570422-21570593172SH2B2_RAT460-517580--
1.9ENSRNOT000000019359ENSRNOE00000013539chr12:21571232-215722311000SH2B2_RAT517-6231071B:4-129

2.1ENST000002640331ENSE00001240819chr11:119076752-119077322571CBL_HUMAN1-65651A:48-6518
2.2ENST000002640332ENSE00001240799chr11:119103158-119103405248CBL_HUMAN66-148831A:66-14883
2.3ENST000002640333ENSE00001240795chr11:119142445-119142591147CBL_HUMAN148-197501A:148-19750
2.4ENST000002640334ENSE00001240790chr11:119144578-119144734157CBL_HUMAN197-249531A:197-24953
2.5ENST000002640335ENSE00001240782chr11:119145542-119145663122CBL_HUMAN250-290411A:250-29041
2.6ENST000002640336ENSE00001240776chr11:119146707-119146844138CBL_HUMAN290-336471A:290-33647
2.7ENST000002640337ENSE00001128289chr11:119148467-11914855488CBL_HUMAN336-365301A:336-35116
2.8ENST000002640338ENSE00001795866chr11:119148876-119149007132CBL_HUMAN366-409440--
2.9ENST000002640339ENSE00001128273chr11:119149220-119149423204CBL_HUMAN410-477680--
2.10ENST0000026403310ENSE00000796209chr11:119155679-119155810132CBL_HUMAN478-521440--
2.11ENST0000026403311ENSE00001206751chr11:119155899-119156276378CBL_HUMAN522-6471260--
2.12ENST0000026403312ENSE00000796211chr11:119158562-11915865695CBL_HUMAN648-679320--
2.13ENST0000026403313ENSE00000796212chr11:119167628-119167744117CBL_HUMAN679-718400--
2.14ENST0000026403314ENSE00000796213chr11:119168094-11916819198CBL_HUMAN718-751340--
2.15ENST0000026403315ENSE00000796214chr11:119169068-119169250183CBL_HUMAN751-812620--
2.16ENST0000026403316ENSE00001238481chr11:119170205-1191776517447CBL_HUMAN812-906950--

(-) 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:304
 aligned with CBL_HUMAN | P22681 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:304
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347    
            CBL_HUMAN    48 PGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG 351
               SCOP domains d1yvha2 A:48-177 N-terminal domain of cbl (N-cbl)                                                                                 d1yvha1 A:178-263 Cbl                                                                 d1yvha3 A:264-351 Cbl                                                                    SCOP domains
               CATH domains 1yvhA01 A:48-175  [code=1.20.930.20, no name defined]                                                                           1yvhA02 A:176-264 EF-hand                                                                1yvhA03 A:265-350 SHC Adaptor Protein                                                 - CATH domains
               Pfam domains Cbl_N-1yvhA03 A:48-176                                                                                                           -Cbl_N2-1yvhA01 A:178-262                                                             -Cbl_N3-1yvhA02 A:264-349                                                              -- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhh...eeehhhhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhh....eeeeee.......eeeeee.....eeee.....hhhhhhhhhhhh....ee........... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1          Exon 2.2  PDB: A:66-148 UniProt: 66-148                                            ------------------------------------------------Exon 2.4  PDB: A:197-249 UniProt: 197-249            Exon 2.5  PDB: A:250-290 UniProt: 250-290---------------------------------------------Exon 2.7         Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------------------------------------------------Exon 2.3  PDB: A:148-197 UniProt: 148-197         --------------------------------------------------------------------------------------------Exon 2.6  PDB: A:290-336 UniProt: 290-336      --------------- Transcript 2 (2)
                 1yvh A  48 PGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG 351
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347    

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with SH2B2_RAT | Q9Z200 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:9
            SH2B2_RAT   612 RAVENQYSF 620
               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 1.9  Transcript 1
                 1yvh B   4 RAVENQySF  12
                                  |  
                                 10-PTR

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (52, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBL_HUMAN | P22681)
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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    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: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:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    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:0045742    positive regulation of epidermal growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0023051    regulation of signaling    Any process that modulates the frequency, rate or extent of a signaling process.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
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:0016600    flotillin complex    A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.
    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.

Chain B   (SH2B2_RAT | Q9Z200)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0035591    signaling adaptor activity    The binding activity of a molecule that brings together two or more molecules in a signaling pathway, permitting those molecules to function in a coordinated way. Adaptor molecules themselves do not have catalytic activity.
    GO:0005068    transmembrane receptor protein tyrosine kinase adaptor activity    The binding activity of a molecule that brings together a transmembrane receptor protein tyrosine kinase and one or more other molecules, permitting them to function in a coordinated way.
biological process
    GO:0001922    B-1 B cell homeostasis    The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity.
    GO:0030036    actin 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 comprising actin filaments and their associated proteins.
    GO:0050851    antigen receptor-mediated signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell.
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0019222    regulation of metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
    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:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBL_HUMAN | P226811b47 1fbv 2cbl 2juj 2k4d 2oo9 2y1m 2y1n 3bum 3bun 3buo 3buw 3bux 3ob1 3ob2 3plf 4a49 4a4b 4a4c 4gpl 5hkw 5hkx 5hky 5hkz 5hl0 5j3x
        SH2B2_RAT | Q9Z2001rpy 1rqq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YVH)