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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 3
 
Authors :  E. Ugochukwu, C. Arrowsmith, A. Barr, G. Bunkoczi, S. Das, J. Debreczen A. Edwards, J. Eswaran, S. Knapp, M. Sundstrom, A. Turnbull, F. Von De J. Weigelt, Structural Genomics Consortium (Sgc)
Date :  23 Sep 05  (Deposition) - 04 Oct 05  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Phosphatase, Non-Receptor Type, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Muller, S. Knapp
Large-Scale Structural Analysis Of The Classical Human Protein Tyrosine Phosphatome.
Cell(Cambridge, Mass. ) V. 136 352 2009
PubMed-ID: 19167335  |  Reference-DOI: 10.1016/J.CELL.2008.11.038

(-) Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 3
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLIC-SGC1
    FragmentCATALYTIC DOMAIN
    GenePTPN3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B49)

(-) Sites  (0, 0)

(no "Site" information available for 2B49)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B49)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:761 -Pro A:762

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055256D763NPTN3_HUMANPolymorphism10116806AD763N

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN3_HUMAN646-901  1A:646-901
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN3_HUMAN819-892  1A:819-892
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN3_HUMAN840-850  1A:840-850

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003745411bENSE00001463801chr9:112260586-11226049988PTN3_HUMAN-00--
1.2aENST000003745412aENSE00001463800chr9:112225737-112225577161PTN3_HUMAN1-46460--
1.3ENST000003745413ENSE00001681728chr9:112219679-112219572108PTN3_HUMAN47-82360--
1.4ENST000003745414ENSE00001733651chr9:112219495-11221945343PTN3_HUMAN83-97150--
1.5ENST000003745415ENSE00001689765chr9:112216854-11221677679PTN3_HUMAN97-123270--
1.6bENST000003745416bENSE00001788195chr9:112211135-11221109145PTN3_HUMAN123-138160--
1.7ENST000003745417ENSE00001625396chr9:112207572-11220752053PTN3_HUMAN138-156190--
1.8ENST000003745418ENSE00001606103chr9:112200514-112200394121PTN3_HUMAN156-196410--
1.9ENST000003745419ENSE00001747223chr9:112199250-11219916388PTN3_HUMAN196-225300--
1.10ENST0000037454110ENSE00001750132chr9:112195441-11219535389PTN3_HUMAN226-255300--
1.11ENST0000037454111ENSE00000983477chr9:112190964-11219090164PTN3_HUMAN255-276220--
1.12ENST0000037454112ENSE00000983478chr9:112189402-112189230173PTN3_HUMAN277-334580--
1.13ENST0000037454113ENSE00000806056chr9:112185132-112184998135PTN3_HUMAN334-379460--
1.14ENST0000037454114ENSE00000806055chr9:112182880-112182704177PTN3_HUMAN379-438600--
1.15ENST0000037454115ENSE00001090540chr9:112172695-112172509187PTN3_HUMAN438-500630--
1.16ENST0000037454116ENSE00001090547chr9:112172356-11217227978PTN3_HUMAN501-526260--
1.17ENST0000037454117ENSE00001090546chr9:112170657-11217060157PTN3_HUMAN527-545190--
1.18ENST0000037454118ENSE00001090539chr9:112168898-112168742157PTN3_HUMAN546-598530--
1.19ENST0000037454119ENSE00001090545chr9:112166888-112166728161PTN3_HUMAN598-651541A:646-6516
1.22ENST0000037454122ENSE00001090543chr9:112153841-11215375191PTN3_HUMAN652-682311A:652-68231
1.23ENST0000037454123ENSE00001090536chr9:112153479-11215341862PTN3_HUMAN682-702211A:682-70221
1.24bENST0000037454124bENSE00001090538chr9:112151659-112151513147PTN3_HUMAN703-751491A:703-75149
1.25aENST0000037454125aENSE00001090542chr9:112145831-112145703129PTN3_HUMAN752-794431A:752-79443
1.26ENST0000037454126ENSE00001732241chr9:112144727-112144582146PTN3_HUMAN795-843491A:795-84349
1.27ENST0000037454127ENSE00001661887chr9:112144067-112143932136PTN3_HUMAN843-888461A:843-88846
1.28bENST0000037454128bENSE00001463784chr9:112141913-1121379793935PTN3_HUMAN889-913251A:889-90416

(-) 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:259
 aligned with PTN3_HUMAN | P26045 from UniProtKB/Swiss-Prot  Length:913

    Alignment length:259
                                   655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895         
           PTN3_HUMAN   646 VLIQFEQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANLVNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYEE 904
               SCOP domains d2b49a_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2b49A00 A:646-904 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.........hhhhhhhhhhhh...........eee......eeeeeeeeeeehhhheeeeeeee......hhhhhhhhhhhh...eeee....ee..ee...........eeee..eeeeeeeeee...eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_PTP  PDB: A:646-901 UniProt: 646-901                                                                                                                                                                                                            --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:819-892 UniProt: 819-892                        ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
           Transcript 1 (1) 1.19  Exon 1.22  PDB: A:652-682      --------------------Exon 1.24b  PDB: A:703-751 UniProt: 703-751      Exon 1.25a  PDB: A:752-794 UniProt: 752-794Exon 1.26  PDB: A:795-843 UniProt: 795-843       ---------------------------------------------Exon 1.28b       Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.23            --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.27  PDB: A:843-888 UniProt: 843-888    ---------------- Transcript 1 (2)
                 2b49 A 646 VLIQFEQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANLVNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYEE 904
                                   655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895         

   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 2B49)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN3_HUMAN | P26045)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    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: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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0017080    sodium channel regulator activity    Modulates the activity of a sodium channel.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:0051045    negative regulation of membrane protein ectodomain proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of membrane protein ectodomain proteolysis.
    GO:0045930    negative regulation of mitotic cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
    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:0098902    regulation of membrane depolarization during action potential    Any process that modulates the rate, frequency or extent of membrane depolarization during an action potential. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential.
    GO:2000649    regulation of sodium ion transmembrane transporter activity    Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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  Cis Peptide Bonds
    Pro A:761 - Pro A:762   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN3_HUMAN | P260454qum 4qun 4rh5 4rh9 4rhg 4ri4 4ri5 4s0g

(-) Related Entries Specified in the PDB File

1l8k T CELL PROTEIN-TYROSINE PHOSPHATASE STRUCTURE