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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN OF T-CELL LYMPHOMA INVASION AND METASTASIS 1 VARIAN
 
Authors :  X. R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Dec 05  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, T-Cell Lymphoma Invasion And Metastasis 1 Variant, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Immune System, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain Of T-Cell Lymphoma Invasion And Metastasis 1 Varian
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T-CELL LYMPHOMA INVASION AND METASTASIS 1 VARIANT
    ChainsA
    EngineeredYES
    Expression System PlasmidP050425-07
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneT1AM-1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2D8I)

(-) Sites  (0, 0)

(no "Site" information available for 2D8I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D8I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D8I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051993Q844HTIAM1_HUMANPolymorphism16987932AQ17H

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.TIAM1_HUMAN845-908  1A:18-81

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002868272ENSE00001372551chr21:32931290-3293124051TIAM1_HUMAN-00--
1.3ENST000002868273ENSE00001367893chr21:32836348-3283629653TIAM1_HUMAN-00--
1.5ENST000002868275ENSE00001383160chr21:32711737-32711558180TIAM1_HUMAN-00--
1.6ENST000002868276ENSE00001365575chr21:32649224-32649048177TIAM1_HUMAN-00--
1.7bENST000002868277bENSE00001025653chr21:32639299-32638326974TIAM1_HUMAN1-3213210--
1.8ENST000002868278ENSE00001025652chr21:32624505-32624058448TIAM1_HUMAN322-4711500--
1.9ENST000002868279ENSE00001025654chr21:32617976-32617804173TIAM1_HUMAN471-528580--
1.10ENST0000028682710ENSE00001025660chr21:32598266-32598042225TIAM1_HUMAN529-603750--
1.11ENST0000028682711ENSE00001025647chr21:32595907-32595722186TIAM1_HUMAN604-665620--
1.12ENST0000028682712ENSE00001025659chr21:32590015-32589869147TIAM1_HUMAN666-714490--
1.13aENST0000028682713aENSE00001265070chr21:32585788-3258571475TIAM1_HUMAN715-739250--
1.14ENST0000028682714ENSE00001025641chr21:32582531-32582361171TIAM1_HUMAN740-796571A:1-44
1.15ENST0000028682715ENSE00001025658chr21:32575328-32575224105TIAM1_HUMAN797-831351A:5-73
1.16ENST0000028682716ENSE00001025636chr21:32567621-3256754082TIAM1_HUMAN832-859281A:8-3225
1.17ENST0000028682717ENSE00001025648chr21:32559403-3255931787TIAM1_HUMAN859-888301A:32-6130
1.18ENST0000028682718ENSE00001025649chr21:32554962-32554738225TIAM1_HUMAN888-963761A:61-111 (gaps)75
1.19ENST0000028682719ENSE00001025650chr21:32537382-32537279104TIAM1_HUMAN963-997351A:112-1143
1.20ENST0000028682720ENSE00001025643chr21:32526744-32526565180TIAM1_HUMAN998-1057600--
1.21ENST0000028682721ENSE00001025638chr21:32525452-3252538469TIAM1_HUMAN1058-1080230--
1.22ENST0000028682722ENSE00001025637chr21:32525079-32524954126TIAM1_HUMAN1081-1122420--
1.23bENST0000028682723bENSE00001025651chr21:32519321-32519213109TIAM1_HUMAN1123-1159370--
1.24ENST0000028682724ENSE00001610053chr21:32513822-32513643180TIAM1_HUMAN1159-1219610--
1.25ENST0000028682725ENSE00001722006chr21:32513554-32513436119TIAM1_HUMAN1219-1258400--
1.26ENST0000028682726ENSE00001700177chr21:32508359-32508251109TIAM1_HUMAN1259-1295370--
1.27ENST0000028682727ENSE00001806004chr21:32503266-3250320859TIAM1_HUMAN1295-1314200--
1.28aENST0000028682728aENSE00001667545chr21:32502633-32502531103TIAM1_HUMAN1315-1349350--
1.29ENST0000028682729ENSE00001597652chr21:32499470-3249938388TIAM1_HUMAN1349-1378300--
1.30aENST0000028682730aENSE00001769773chr21:32497012-32496840173TIAM1_HUMAN1378-1436590--
1.31bENST0000028682731bENSE00001612577chr21:32493155-324907342422TIAM1_HUMAN1436-15911560--

(-) 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:114
 aligned with TIAM1_HUMAN | Q13009 from UniProtKB/Swiss-Prot  Length:1591

    Alignment length:191
                                   793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973 
          TIAM1_HUMAN   784 GDTARDTLELICKTHQLDHSAHYLRLKFLIENKMQLYVPQPEEDIYELLYKEIEICPKVTQSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMLKDFLSQPSLGLLVRTYPELEEGVELLESPPHRVDGPADLGESPLAFLTSNPGHSLCSEQGSSA 974
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....--------------...------------------------------.......eeeeeeee...........eeeeeee..eeeeeeee.....hhhhhh......eeee...hhhhhhhhhhhhhhh..eeeeeeee.........------------------------...---------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------PDZ  PDB: A:18-81 UniProt: 845-908                              ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.14    Exon 1.15  PDB: A:5-7 [INCOMPLETE] Exon 1.16  PDB: A:8-32      ----------------------------Exon 1.18  PDB: A:61-111 (gaps) UniProt: 888-963 [INCOMPLETE]               ----------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.17  PDB: A:32-61       --------------------------------------------------------------------------Exon 1.19    Transcript 1 (2)
                 2d8i A   1 GSSG--------------SSG------------------------------EIEICPKVTQSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMLKDFLSQPSLGLLVRTYPELEEGVE------------------------SGP---------SSG 114
                               |     -        |6|        -         -         - |      16        26        36        46        56        66        76        86        96       106 |       -         -      | |-       113 
                               4              5 7                              8                                                                                                 108                      109 |       112  
                                                                                                                                                                                                            111            

   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 2D8I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D8I)

(-) Gene Ontology  (55, 55)

NMR Structure(hide GO term definitions)
Chain A   (TIAM1_HUMAN | Q13009)
molecular function
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0030676    Rac guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0017016    Ras GTPase binding    Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
biological process
    GO:0016601    Rac protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state.
    GO:0060071    Wnt signaling pathway, planar cell polarity pathway    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    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:0003300    cardiac muscle hypertrophy    The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
    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:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    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:1990138    neuron projection extension    Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043507    positive regulation of JUN kinase activity    Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
    GO:1904268    positive regulation of Schwann cell chemotaxis    Any process that activates or increases the frequency, rate or extent of Schwann cell chemotaxis.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0061003    positive regulation of dendritic spine morphogenesis    Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is 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:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0072657    protein localization to membrane    A process in which a protein is transported to, or maintained in, a specific location in a membrane.
    GO:0070372    regulation of ERK1 and ERK2 cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:1904338    regulation of dopaminergic neuron differentiation    Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation.
    GO:0061178    regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:2000050    regulation of non-canonical Wnt signaling pathway    Any process that modulates the frequency, rate or extent of non-canonical Wnt signaling pathway.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0042220    response to cocaine    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 cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
    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:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    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:0044291    cell-cell contact zone    Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0044304    main axon    The main axonal trunk, as opposed to the collaterals; i.e., excluding collaterals, terminal, spines, or dendrites.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0036477    somatodendritic compartment    The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TIAM1_HUMAN | Q130093kzd 3kze 4gvc 4gvd 4k2o 4k2p 4nxp 4nxq 4nxr

(-) Related Entries Specified in the PDB File

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