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(-) Description

Title :  NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR
 
Authors :  S. Frese, W. -D. Schubert, A. C. Findeis, T. Marquardt, Y. S. Roske, T. E. B. Stradal, D. W. Heinz
Date :  17 Mar 06  (Deposition) - 24 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,L,M
Biol. Unit 1:  A,L  (1x)
Biol. Unit 2:  B,M  (1x)
Keywords :  Protein-Binding, Sh2-Domain/Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Frese, W. -D. Schubert, A. C. Findeis, T. Marquardt, Y. S. Roske, T. E. B. Stradal, D. W. Heinz
The Phosphotyrosine Peptide Binding Specificity Of Nck1 And Nck2 Src Homology 2 Domains.
J. Biol. Chem. V. 281 18236 2006
PubMed-ID: 16636066  |  Reference-DOI: 10.1074/JBC.M512917200

(-) Compounds

Molecule 1 - CYTOPLASMIC PROTEIN NCK1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1 (AMERSHAM BIOSCIENCES)
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentSH2-DOMAIN, RESIDUES 281-377
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCK ADAPTOR PROTEIN 1, SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA
 
Molecule 2 - TRANSLOCATED INTIMIN RECEPTOR
    ChainsL, M
    FragmentPHOSPHOPEPTIDE LIGAND OF NCK-SH2, RESIDUES 469-480
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsTHE PEPTIDE WAS SYNTHESIZED CHEMICALLY
    StrainEPEC E2348/69 (O127:H6)
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABLM
Biological Unit 1 (1x)A L 
Biological Unit 2 (1x) B M

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 2CI9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CI9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln B:366 -Gly B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CI9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.NCK1_HUMAN282-376
 
  2A:282-376
B:282-376
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.NCK1_HUMAN282-376
 
  1A:282-376
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.NCK1_HUMAN282-376
 
  1-
B:282-376

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002889861aENSE00001809490chr3:136581050-136581161112NCK1_HUMAN-00--
1.4aENST000002889864aENSE00002146254chr3:136646826-136647069244NCK1_HUMAN1-76760--
1.6dENST000002889866dENSE00001036982chr3:136664425-136665137713NCK1_HUMAN76-3132382A:276-313 (gaps)
B:277-313 (gaps)
61
60
1.8bENST000002889868bENSE00001154745chr3:136667101-136667968868NCK1_HUMAN314-377642A:314-377
B:314-377
64
64

(-) Sequences/Alignments

Asymmetric 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:102
 aligned with NCK1_HUMAN | P16333 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:125
                                   262       272       282       292       302       312       322       332       342       352       362       372     
           NCK1_HUMAN   253 NPLTSGLEPSPPQCDYIRPSLTGKFAGNPWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-----------------------.......hhhhhhhhhhh.....eeeeeee.....eeeeeeee..eeeeeee.....eeee..eee.hhhhhhhhhhhh..eee...eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------SH2  PDB: A:282-376 UniProt: 282-376                                                           - PROSITE
               Transcript 1 Exon 1.6d  PDB: A:276-313 (gaps) UniProt: 76-313 [INCOMPLETE]Exon 1.8b  PDB: A:314-377 UniProt: 314-377                       Transcript 1
                 2ci9 A 276 GPLGS-----------------------PWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS 377
                                |    -         -       282       292       302       312       322       332       342       352       362       372     
                              280                     281                                                                                                

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with NCK1_HUMAN | P16333 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:124
                                   263       273       283       293       303       313       323       333       343       353       363       373    
           NCK1_HUMAN   254 PLTSGLEPSPPQCDYIRPSLTGKFAGNPWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS 377
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------------------................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SH2  PDB: B:282-376 UniProt: 282-376                                                           - PROSITE
               Transcript 1 Exon 1.6d  PDB: B:277-313 (gaps) UniProt: 76-313            Exon 1.8b  PDB: B:314-377 UniProt: 314-377                       Transcript 1
                 2ci9 B 277 PLGS-----------------------PWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS 377
                               |     -         -       283       293       303       313       323       333       343       353       363       373    
                             280                     281                                                                                                

Chain L from PDB  Type:PROTEIN  Length:9
 aligned with TIR_ECO27 | B7UM99 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:9
            TIR_ECO27   472 HIYDEVAAD 480
               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
                 2ci9 L 472 HIyDEVAAD 480
                              |      
                            474-PTR  

Chain M from PDB  Type:PROTEIN  Length:12
 aligned with TIR_ECO27 | B7UM99 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:12
                                   479  
            TIR_ECO27   470 EEHIYDEVAADP 481
               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
                 2ci9 M 470 EEHIyDEVAADP 481
                                |  479  
                              474-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  (0, 0)

(no "SCOP Domain" information available for 2CI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CI9)

(-) Gene Ontology  (54, 55)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NCK1_HUMAN | P16333)
molecular function
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. 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: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:0008093    cytoskeletal adaptor activity    The binding activity of a molecule that brings together a cytoskeletal protein and one or more other molecules, permitting them to function in a coordinated way.
    GO:0071074    eukaryotic initiation factor eIF2 binding    Interacting selectively and non-covalently with eukaryotic initiation factor eIF2, a protein complex involved in the initiation of ribosome-mediated translation.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004860    protein kinase inhibitor activity    Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
biological process
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    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:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0007015    actin filament 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. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    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:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:1903898    negative regulation of PERK-mediated unfolded protein response    Any process that stops, prevents or reduces the frequency, rate or extent of the PERK-mediated unfolded protein response.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1903912    negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation    Any process that stops, prevents or reduces the frequency, rate or extent of endoplasmic reticulum stress-induced eiF2alpha phosphorylation.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:1990441    negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an endoplasmic reticulum stress.
    GO:0070262    peptidyl-serine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-L-serine to form peptidyl-serine.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:1903676    positive regulation of cap-dependent translational initiation    Any process that activates or increases the frequency, rate or extent of cap-dependent translational initiation.
    GO:1903679    positive regulation of cap-independent translational initiation    Any process that activates or increases the frequency, rate or extent of cap-independent translational initiation.
    GO:1902237    positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0036493    positive regulation of translation in response to endoplasmic reticulum stress    Any process that activates, or increases the frequency, rate or extent of translation as a result of endoplasmic reticulum stress.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0051707    response to other organism    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 stimulus from another living organism.
    GO:0007172    signal complex assembly    The aggregation, arrangement and bonding together of a set of components to form a complex capable of relaying a signal within a cell.
    GO:0006930    substrate-dependent cell migration, cell extension    The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0000164    protein phosphatase type 1 complex    A protein complex that possesses magnesium-dependent protein serine/threonine phosphatase (AMD phosphatase) activity, and consists of a catalytic subunit and one or more regulatory subunits that dictates the phosphatase's substrate specificity, function, and activity.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0012506    vesicle membrane    The lipid bilayer surrounding any membrane-bounded vesicle in the cell.

Chain L,M   (TIR_ECO27 | B7UM99)
molecular function
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCK1_HUMAN | P163332ci8 2cub 2js0 2js2 2jw4
        TIR_ECO27 | B7UM992cia

(-) Related Entries Specified in the PDB File

2ci8 NCK1-SH2 DOMAIN - ESTABLISHING THE PHOSPHOTYROSINE PEPTIDE BINDING SPECIFICITIES OF NCK1 AND NCK2 SH2 DOMAINS
2cia NCK2 SH2-DOMAIN IN COMPLEX WITH A DECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR
2cub SOLUTION STRUCTURE OF THE SH3 DOMAIN OF THE HUMANCYTOPLASMIC PROTEIN NCK1