Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Authors :  A. J. Barr, J. E. Debreczeni, J. Eswaran, C. Smee, N. Burgess, O. Gileadi M. Sundstrom, C. Arrowsmith, A. Edwards, S. Knapp, F. Von Delft
Date :  21 Jan 05  (Deposition) - 17 Mar 05  (Release) - 13 Jul 11  (Revision)
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Ptpn5, Step, Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  J. Eswaran, J. P. Von Kries, B. Marsden, E. Longman, J. E. Debreczeni, E. Ugochukwu, A. Turnbull, W. H. Lee, S. Knapp, A. J. Barr
Crystal Structures And Inhibitor Identification For Ptpn5, Ptprr And Ptpn7: A Family Of Human Mapk- Specific Protein Tyrosine Phosphatases.
Biochem. J. V. 395 483 2006
PubMed-ID: 16441242  |  Reference-DOI: 10.1042/BJ20051931

(-) Compounds

    EC Number3.1.3.48
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineDE3
    Expression System PlasmidPLIC SGC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorT7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Ser A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN5_HUMAN300-555  1A:276-531
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN5_HUMAN469-546  1A:445-522
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN5_HUMAN494-504  1A:470-480

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:284
 aligned with PTN5_HUMAN | P54829 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:287
                                   284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       
               SCOP domains d2bija_ A: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2bijA00 A:-7-537 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh.hhhhhhhhhh.......hhhhh...hhhhhh.......hhh.eee.......hhhhheeeeeee.hhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeee.....---.........eeee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_PTP  PDB: A:276-531 UniProt: 300-555                                                                                                                                                                                                            ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:445-522 UniProt: 469-546                            --------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.8b  PDB: A:-7-281       ----------------------------Exon 1.10  PDB: A:310-336  Exon 1.11  PDB: A:337-379 UniProt: 361-406    Exon 1.12  PDB: A:383-419            Exon 1.13b  PDB: A:420-473 UniProt: 444-497           -------------------------------------Exon 1.15c  PDB: A:511-537  Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.9  PDB: A:282-310     ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:473-511              -------------------------- Transcript 1 (2)
                                  |260       270       280       290       300       310       320       330       340       350       360       370        |-  |    390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       
                                 -1|                                                                                                                      379 383                                                                                                                                                          

   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 2BIJ)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN5_HUMAN | P54829)
molecular function
    GO:0035254    glutamate receptor binding    Interacting selectively and non-covalently with a glutamate receptor.
    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:0051019    mitogen-activated protein kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase.
    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:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0035640    exploration behavior    The specific behavior of an organism in response to a novel environment or stimulus.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1900273    positive regulation of long-term synaptic potentiation    Any process that activates or increases the frequency, rate or extent of long-term synaptic potentiation.
    GO:1901216    positive regulation of neuron death    Any process that activates or increases the frequency, rate or extent of neuron death.
    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:0033160    positive regulation of protein import into nucleus, translocation    Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:2001025    positive regulation of response to drug    Any process that activates or increases the frequency, rate or extent of response to drug.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:1903492    response to acetylsalicylate    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 an aspirin (acetylsalicylate) stimulus. Aspirin is a non-steroidal anti-inflammatory drug with moA cyclooxygenase inhibitor activity.
    GO:0001975    response to amphetamine    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 an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0035902    response to immobilization stress    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 being rendered immobile.
cellular component
    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: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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:1990635    proximal dendrite    That part of the dendrite closest to the cell body of the neuron.


(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
    Ser A:319 - Pro A:320   [ RasMol ]  

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  PTN5_HUMAN | P54829
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  PTN5_HUMAN | P54829
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        PTN5_HUMAN | P548292bv5 2cjz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BIJ)