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(-) Description

Title :  STRUCTURE OF THE CATALYTIC DOMAIN OF THE CHICK RETINAL NEURITE INHIBITOR-RECEPTOR PROTEIN TYROSINE PHOSPHATASE CRYP-2/CPTPRO
 
Authors :  T. S. Girish, B. Gopal
Date :  13 Apr 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Tyrosine Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. S. Girish, B. Gopal
The Crystal Structure Of The Catalytic Domain Of The Chick Retinal Neurite Inhibitor-Receptor Protein Tyrosine Phosphatase Cryp-2/Cptpro
Proteins V. 68 1011 2007
PubMed-ID: 17546659  |  Reference-DOI: 10.1002/PROT.21424
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE CRYP-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-22B
    Expression System StrainT7 POLYMERASE
    Expression System Taxid562
    Expression System Vector TypePET
    FragmentCATALYTIC DOMAIN, RESIDUES 956-1267
    GeneCRYP2
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1153 , CYS A:1187 , SER A:1188 , ALA A:1189 , GLY A:1190 , VAL A:1191 , GLY A:1192 , ARG A:1193BINDING SITE FOR RESIDUE NO3 A 2001
2AC2SOFTWARECYS B:1187 , SER B:1188 , ALA B:1189 , GLY B:1190 , VAL B:1191 , GLY B:1192 , ARG B:1193BINDING SITE FOR RESIDUE NO3 B 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PI7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:1156 -Pro B:1157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PI7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PI7)

(-) Exons   (0, 0)

(no "Exon" information available for 2PI7)

(-) 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:294
 aligned with Q98945_CHICK | Q98945 from UniProtKB/TrEMBL  Length:1267

    Alignment length:294
                                   969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249    
        Q98945_CHICK    960 LKKRKLTNPVQLDDFDGYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPMNRCKNRYTNILPYDFSRVRLVSMNEEEGSDYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEDPIAYGDITVEMLSEEEHTDWVYRNFRISYADEVQDVMHFNYTAWPDHGVPTANAAESILQFVQMVRQKSVKSKGPMIIHCSAGVGRTGTFIALDWLLQHIRDHEFVDILGLVSDMRSYRMSMVQTEEQYIFIHQCVQLMWQKKKQQ 1253
               SCOP domains d2pi7a_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2pi7A00 A:960-1253 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh............................eeee........eeee......hhhhhhhhhhhh...eeee....ee..ee............eee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee............hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pi7 A  960 LKKRKLTNPVQLDDFDGYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPMNRCKNRYTNILPYDFSRVRLVSMNEEEGSDYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEDPIAYGDITVEMLSEEEHTDWVYRNFRISYADEVQDVMHFNYTAWPDHGVPTANAAESILQFVQMVRQKSVKSKGPMIIHCSAGVGRTGTFIALDWLLQHIRDHEFVDILGLVSDMRSYRMSMVQTEEQYIFIHQCVQLMWQKKKQQ 1253
                                   969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249    

Chain B from PDB  Type:PROTEIN  Length:289
 aligned with Q98945_CHICK | Q98945 from UniProtKB/TrEMBL  Length:1267

    Alignment length:289
                                   972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242         
        Q98945_CHICK    963 RKLTNPVQLDDFDGYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPMNRCKNRYTNILPYDFSRVRLVSMNEEEGSDYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEDPIAYGDITVEMLSEEEHTDWVYRNFRISYADEVQDVMHFNYTAWPDHGVPTANAAESILQFVQMVRQKSVKSKGPMIIHCSAGVGRTGTFIALDWLLQHIRDHEFVDILGLVSDMRSYRMSMVQTEEQYIFIHQCVQLMWQKKK 1251
               SCOP domains d2pi7b_ B: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2pi7B00 B:963-1251 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) --------------------------------------------------Y_phosphatase-2pi7B01 B:1013-1245                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------Y_phosphatase-2pi7B02 B:1013-1245                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author ......ee..hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh............................eeee........eeee......hhhhhhhhhhhh...eeee....ee..ee............eee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee.............hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pi7 B  963 RKLTNPVQLDDFDGYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPMNRCKNRYTNILPYDFSRVRLVSMNEEEGSDYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEDPIAYGDITVEMLSEEEHTDWVYRNFRISYADEVQDVMHFNYTAWPDHGVPTANAAESILQFVQMVRQKSVKSKGPMIIHCSAGVGRTGTFIALDWLLQHIRDHEFVDILGLVSDMRSYRMSMVQTEEQYIFIHQCVQLMWQKKK 1251
                                   972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q98945_CHICK | Q98945)
molecular function
    GO:0017147    Wnt-protein binding    Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0072112    glomerular visceral epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells.
    GO:0032835    glomerulus development    The progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney. The glomerulus is part of the nephron and is restricted to one body segment.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0008045    motor neuron axon guidance    The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0003105    negative regulation of glomerular filtration    Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases 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:0090260    negative regulation of retinal ganglion cell axon guidance    Any process that decreases the frequency, rate, or extent of retinal ganglion cell axon guidance, the process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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:0003093    regulation of glomerular filtration    Any process that modulates the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process in which blood is filtered by the glomerulus into the renal tubule.
    GO:0036060    slit diaphragm assembly    The aggregation, arrangement and bonding together of a set of components to form a slit diaphragm, specialized cell-cell junction found between the interdigitating foot processes of the glomerular epithelium (the podocytes) in the vertebrate kidney, which is adapted for facilitating glomerular filtration.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    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: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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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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