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(-) Description

Title :  HUMAN NEDD4 3RD WW DOMAIN COMPLEX WITH EBOLA ZAIRE VIRUS MATRIX PROTEIN VP40 DERIVED PEPTIDE ILPTAPPEYMEA
 
Authors :  M. Iglesias-Bexiga, M. Macias, R. Bonet, F. J. Blanco, E. S. Cobos, I. Lu
Date :  23 Oct 09  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Ww Domain, Complex, Virus L Domain, Nedd4, Ebola, Host-Virus Interaction, Ligase, Phosphoprotein, Ubl Conjugation Pathway, Cell Membrane, Ribonucleoprotein, Rna Replication, Rna-Binding, Viral Matrix Protein, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Iglesias-Bexiga
Human Nedd4 3Rd Ww Domain Complex With Ebola Zaire Virus Matrix Protein Vp40 Derived Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE NEDD4
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid469008
    Expression System VariantBL21(DE3)
    Expression System VectorPETM11
    Expression System Vector TypeVECTOR
    Fragment3RD WW DOMAIN, UNP RESIDUES 834-878
    GeneNEDD4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN- REGULATED PROTEIN 4, NEDD-4, CELL PROLIFERATION-INDUCING GENE 53 PROTEIN
 
Molecule 2 - 12-MER FROM MATRIX PROTEIN VP40
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 5-16
    Organism CommonHTLV-1
    Organism ScientificHUMAN T-CELL LYMPHOTROPHIC VIRUS TYPE 1 ISOLATE MEL 15
    Organism Taxid402046
    Other DetailsCHEMICAL SYNTHESIS
    SynonymMEMBRANE-ASSOCIATED PROTEIN VP40
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KQ0)

(-) Sites  (0, 0)

(no "Site" information available for 2KQ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KQ0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.NEDD4_HUMAN616-641
773-798
846-871
898-923
  1-
-
A:17-42
-
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.NEDD4_HUMAN616-641
773-798
846-871
898-923
  1-
-
A:17-42
-

(-) Exons   (0, 0)

(no "Exon" information available for 2KQ0)

(-) Sequences/Alignments

NMR Structure
   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:35
 aligned with NEDD4_HUMAN | P46934 from UniProtKB/Swiss-Prot  Length:1319

    Alignment length:35
                                   850       860       870     
          NEDD4_HUMAN   841 FLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPRLKI 875
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains -WW-2kq0A01 A:13-42            ---- Pfam domains
         Sec.struct. author .....eeeeee...eeeeee....eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE -----WW_DOMAIN_1  PDB: A:17-42 ---- PROSITE
                 Transcript ----------------------------------- Transcript
                 2kq0 A  12 FLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPRLKI  46
                                    21        31        41     

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with VP40_EBOZM | Q05128 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:9
           VP40_EBOZM     8 TAPPEYMEA  16
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2kq0 B 112 TAPPEYMEA 120

   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 2KQ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KQ0)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (83, 86)

NMR Structure(hide GO term definitions)
Chain A   (NEDD4_HUMAN | P46934)
molecular function
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0031698    beta-2 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-2 adrenergic 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:0050815    phosphoserine residue binding    Interacting selectively and non-covalently with a phosphorylated serine residue within a protein.
    GO:0050816    phosphothreonine residue binding    Interacting selectively and non-covalently with a phosphorylated threonine residue within a protein.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019871    sodium channel inhibitor activity    Stops, prevents, or reduces the activity of a sodium channel.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    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.
biological process
    GO:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    GO:0034644    cellular response to UV    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0044111    development involved in symbiotic interaction    The progression of an organism from an initial condition to a later condition, occurring when the organism is in a symbiotic interaction.
    GO:0003197    endocardial cushion development    The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
    GO:0042921    glucocorticoid receptor signaling pathway    Any series of molecular signals generated as a consequence of a glucocorticoid binding to its receptor.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0007041    lysosomal transport    The directed movement of substances into, out of or within a lysosome.
    GO:2000650    negative regulation of sodium ion transmembrane transporter activity    Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity.
    GO:0010766    negative regulation of sodium ion transport    Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0010768    negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage    Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus.
    GO:0030948    negative regulation of vascular endothelial growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    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:0007528    neuromuscular junction development    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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:0046824    positive regulation of nucleocytoplasmic transport    Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.
    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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0050847    progesterone receptor signaling pathway    Any series of molecular signals generated as a consequence of a progesterone binding to its receptor.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    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:0032801    receptor catabolic process    The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0048814    regulation of dendrite morphogenesis    Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0016241    regulation of macroautophagy    Any process that modulates the frequency, rate or extent of macroautophagy.
    GO:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:1901016    regulation of potassium ion transmembrane transporter activity    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transporter activity.
    GO:0050807    regulation of synapse organization    Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0014894    response to denervation involved in regulation of muscle adaptation    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 denervation stimulus. This process occurs as part of the regulation of muscle adaptation.
    GO:0019089    transmission of virus    The transfer of virions in order to create new infection.
    GO:0043162    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0016327    apicolateral plasma membrane    The apical end of the lateral plasma membrane of epithelial cells.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    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: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:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

Chain B   (VP40_EBOZM | Q05128)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
biological process
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0044414    suppression of host defenses    Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host defense(s) by active mechanisms that normally result in the shutting down of a host pathway. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0033645    host cell endomembrane system    A collection of membranous structures involved in transport within the host cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044185    host cell late endosome membrane    The lipid bilayer surrounding a host cell late endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0044385    integral to membrane of host cell    Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEDD4_HUMAN | P469342kpz 2m3o 2xbb 2xbf 3b7y 4bbn 4be8 4n7f 4n7h 5aht 5c7j 5c91
        VP40_EBOZM | Q051281h2c 1h2d 4eje 4ldb 4ldd 4ldi 4ldm

(-) Related Entries Specified in the PDB File

2kpz THE SAME PROTEIN COMPLEXED WITH ANOTHER PEPTIDE