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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE KAPPA AT 1.95A RESOLUTION
 
Authors :  J. E. Debreczeni, E. Ugochukwu, J. Eswaran, A. Barr, S. Das, N. Burgess, O. Gileadi, E. Longman, F. Von Delft, S. Knapp, M. Sundstron, C. Arrow J. Weigelt, A. Edwards
Date :  28 Nov 05  (Deposition) - 02 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Receptor Type Tyrosine Phosphatase Kappa, Ptprk, Glycoprotein, Hydrolase, Immunoglobulin Domain, Protein Phosphatase, Receptor, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Eswaran, J. E. Debreczeni, E. Longman, A. Barr, S. Knapp
The Crystal Structure Of Human Receptor Protein Tyrosine Kappa Phosphatase Kappa Domain 1.
Protein Sci. V. 15 1500 2006
PubMed-ID: 16672235  |  Reference-DOI: 10.1110/PS.062128706

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE KAPPA
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineDE3
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 865-1154
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN PROTEIN TYROSINE PHOSPHATASE KAPPA, PROTEIN-TYROSINE PHOSPHATASE KAPPA, R-PTP-KAPPA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1083 , SER A:1084 , ALA A:1085 , GLY A:1086 , ALA A:1087 , GLY A:1088 , ARG A:1089 , GLN A:1127 , HOH A:2121BINDING SITE FOR RESIDUE ACT A2156

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1145 -A:1153

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C7S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C7S)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTPRK_HUMAN887-1141
1173-1435
  1A:888-1142
-
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRK_HUMAN1061-1132
1349-1426
  1A:1062-1133
-
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRK_HUMAN1080-1090
1374-1384
  1A:1081-1091
-

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1kENST000003682151kENSE00001825308chr6:128841503-128841404100PTPRK_HUMAN1-34340--
1.5aENST000003682155aENSE00002199653chr6:128718833-128718711123PTPRK_HUMAN34-75420--
1.6bENST000003682156bENSE00002180599chr6:128643455-128643184272PTPRK_HUMAN75-165910--
1.7ENST000003682157ENSE00002186216chr6:128563747-12856366682PTPRK_HUMAN166-193280--
1.9ENST000003682159ENSE00002195257chr6:128561295-128561180116PTPRK_HUMAN193-231390--
1.13bENST0000036821513bENSE00002199647chr6:128540241-128540067175PTPRK_HUMAN232-290590--
1.14bENST0000036821514bENSE00002171628chr6:128505870-128505577294PTPRK_HUMAN290-388990--
1.15ENST0000036821515ENSE00002147298chr6:128411137-128410835303PTPRK_HUMAN388-4891020--
1.16ENST0000036821516ENSE00002171377chr6:128404969-128404860110PTPRK_HUMAN489-525370--
1.17ENST0000036821517ENSE00002142857chr6:128403783-128403582202PTPRK_HUMAN526-593680--
1.18ENST0000036821518ENSE00002147197chr6:128400063-128399958106PTPRK_HUMAN593-628360--
1.19aENST0000036821519aENSE00002140489chr6:128388937-128388664274PTPRK_HUMAN628-719920--
1.20aENST0000036821520aENSE00002180814chr6:128385939-12838590337PTPRK_HUMAN720-732130--
1.23bENST0000036821523bENSE00001446576chr6:128330410-128330275136PTPRK_HUMAN732-777460--
1.26aENST0000036821526aENSE00002158985chr6:128326389-128326229161PTPRK_HUMAN777-831550--
1.30ENST0000036821530ENSE00002188417chr6:128320049-128319865185PTPRK_HUMAN831-892621A:865-89329
1.31ENST0000036821531ENSE00002170574chr6:128318133-12831804688PTPRK_HUMAN893-922301A:894-92330
1.32ENST0000036821532ENSE00002174414chr6:128316683-12831660777PTPRK_HUMAN922-947261A:923-948 (gaps)26
1.34ENST0000036821534ENSE00002154411chr6:128313854-12831381837PTPRK_HUMAN948-960131A:949-96113
1.35ENST0000036821535ENSE00002189670chr6:128312536-12831243998PTPRK_HUMAN960-992331A:961-99333
1.36bENST0000036821536bENSE00002146422chr6:128312030-128311914117PTPRK_HUMAN993-1031391A:994-103239
1.37bENST0000036821537bENSE00002170626chr6:128307020-128306866155PTPRK_HUMAN1032-1083521A:1033-108452
1.38ENST0000036821538ENSE00002152456chr6:128304522-128304387136PTPRK_HUMAN1083-1128461A:1084-112946
1.39ENST0000036821539ENSE00002145193chr6:128304125-128303976150PTPRK_HUMAN1129-1178501A:1130-115526
1.40ENST0000036821540ENSE00002167501chr6:128302434-128302261174PTPRK_HUMAN1179-1236580--
1.41ENST0000036821541ENSE00002162046chr6:128298199-128298068132PTPRK_HUMAN1237-1280440--
1.42ENST0000036821542ENSE00002169316chr6:128297927-128297802126PTPRK_HUMAN1281-1322420--
1.43ENST0000036821543ENSE00002149663chr6:128294972-128294809164PTPRK_HUMAN1323-1377550--
1.44ENST0000036821544ENSE00002147589chr6:128294302-128294167136PTPRK_HUMAN1377-1422460--
1.45bENST0000036821545bENSE00001908169chr6:128291425-128291041385PTPRK_HUMAN1423-1439170--

(-) 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:289
 aligned with PTPRK_HUMAN | Q15262 from UniProtKB/Swiss-Prot  Length:1439

    Alignment length:291
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153 
         PTPRK_HUMAN    864 HPAIRVADLLQHINLMKTSDSYGFKEEYESFFEGQSASWDVAKKDQNRAKNRYGNIIAYDHSRVILQPVEDDPSSDYINANYIDGYQRPSHYIATQGPVHETVYDFWRMIWQEQSACIVMVTNLVEVGRVKCYKYWPDDTEVYGDFKVTCVEMEPLAEYVVRTFTLERRGYNEIREVKQFHFTGWPDHGVPYHATGLLSFIRRVKLSNPPSAGPIVVHCSAGAGRTGCYIVIDIMLDMAEREGVVDIYNCVKALRSRRINMVQTEEQYIFIHDAILEACLCGETAIPVCEF 1154
               SCOP domains d2c7sa_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2c7sA00 A:865-1155 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhhh.......hhhh.......--hhhhhh..eeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee.........eeee..eeeeeeeeee...eeeeeeeeee......eeeeeeee...........hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------TYR_PHOSPHATASE_PTP  PDB: A:888-1142 UniProt: 887-1141                                                                                                                                                                                                         ------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1062-1133 UniProt: 1061-1132                  ---------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.30  PDB: A:865-893    Exon 1.31  PDB: A:894-923     -------------------------Exon 1.34    --------------------------------Exon 1.36b  PDB: A:994-1032            Exon 1.37b  PDB: A:1033-1084 UniProt: 1032-1083     ---------------------------------------------Exon 1.39  PDB: A:1130-115 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.32 UniProt: 922-947------------Exon 1.35  PDB: A:961-993        ------------------------------------------------------------------------------------------Exon 1.38  PDB: A:1084-1129 UniProt: 1083-1128-------------------------- Transcript 1 (2)
                2c7s A  865 MPAIRVADLLQHINLMKTSDSYGFKEEYESFFEGQSASWDVAKKDQNRAKNRYGNIIAYDHSRVILQPV--DPSSDYINANYIDGYQRPSHYIATQGPVHETVYDFWRMIWQEQSACIVMVTNLVEVGRVKCYKYWPDDTEVYGDFKVTCVEMEPLAEYVVRTFTLERRGYNEIREVKQFHFTGWPDHGVPYHATGLLSFIRRVKLSNPPSAGPIVVHCSAGAGRTGCYIVIDIMLDMAEREGVVDIYNCVKALRSRRINMVQTEEQYIFIHDAILEACLCGETAIPVCEF 1155
                                   874       884       894       904       914       924        |- |     944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154 
                                                                                              933  |                                                                                                                                                                                                                           
                                                                                                 936                                                                                                                                                                                                                           

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C7S)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTPRK_HUMAN | Q15262)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0045295    gamma-catenin binding    Interacting selectively and non-covalently with the gamma subunit of the catenin complex.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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: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:0034614    cellular response to reactive oxygen species    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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010839    negative regulation of keratinocyte proliferation    Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0034394    protein localization to cell surface    A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
    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.
    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:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0031256    leading edge membrane    The portion of the plasma membrane surrounding the leading edge of a motile cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0001750    photoreceptor outer segment    The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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