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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN TYROSINE PHOSPHATASE RECEPTOR, TYPE R
 
Authors :  E. Ugochukwu, J. Eswaran, A. Barr, E. Longman, C. Arrowsmith, A. Edward M. Sundstrom, F. Von Delft, S. Knapp, Structural Genomics Consort
Date :  07 Jul 05  (Deposition) - 19 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Phosphatase, Receptor, Human, Structural Genomics, Structural Genomics Consortium, Sgc, 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

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE R
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System VectorPGEX-6P2
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN RESIDUES 375-655
    GenePTPRR, ECPTP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN-TYROSINE PHOSPHATASE PCPTP1, NC-PTPCOM1, CH-1PTPASE

 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
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:459 , GLY A:510 , ILE A:511BINDING SITE FOR RESIDUE CL A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_057141V386IPTPRR_HUMANPolymorphism35387004AV386I
2UniProtVAR_057142V439IPTPRR_HUMANPolymorphism35390084AV439I

  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.PTPRR_HUMAN393-647  1A:393-647
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRR_HUMAN562-638  1A:562-638
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRR_HUMAN586-596  1A:586-596

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002832281ENSE00001252923chr12:71314586-71314113474PTPRR_HUMAN1-20200--
1.2ENST000002832282ENSE00000937354chr12:71286757-71286459299PTPRR_HUMAN20-1191000--
1.4ENST000002832284ENSE00001757470chr12:71158558-71158445114PTPRR_HUMAN120-157380--
1.5ENST000002832285ENSE00001681055chr12:71155406-71155251156PTPRR_HUMAN158-209520--
1.6cENST000002832286cENSE00001616116chr12:71148081-71147971111PTPRR_HUMAN210-246370--
1.7ENST000002832287ENSE00001597238chr12:71139866-71139598269PTPRR_HUMAN247-336900--
1.8ENST000002832288ENSE00001743120chr12:71095103-71094917187PTPRR_HUMAN336-398631A:-1-398 (gaps)40
1.9ENST000002832289ENSE00001615715chr12:71092129-7109204585PTPRR_HUMAN399-427291A:399-42729
1.10ENST0000028322810ENSE00001734453chr12:71078563-7107848480PTPRR_HUMAN427-453271A:427-45327
1.11ENST0000028322811ENSE00001734814chr12:71078044-71077907138PTPRR_HUMAN454-499461A:454-49946
1.12ENST0000028322812ENSE00001713535chr12:71056385-71056275111PTPRR_HUMAN500-536371A:500-53637
1.13ENST0000028322813ENSE00001742676chr12:71054877-71054720158PTPRR_HUMAN537-589531A:537-58953
1.14ENST0000028322814ENSE00001009593chr12:71050597-71050484114PTPRR_HUMAN589-627391A:589-62739
1.15bENST0000028322815bENSE00001252976chr12:71033057-710318621196PTPRR_HUMAN627-657311A:627-65529

(-) 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:283
 aligned with PTPRR_HUMAN | Q15256 from UniProtKB/Swiss-Prot  Length:657

    Alignment length:297
                                   368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       
          PTPRR_HUMAN   359 IPTPREKVAMEYLQSASRILTRSQLRDVVASSHLLQSEFMEIPMNFVDPKEIDIPRHGTKNRYKTILPNPLSRVCLRPKNVTDSLSTYINANYIRGYSGKEKAFIATQGPMINTVDDFWQMVWQEDSPVIVMITKLKEKNEKCVLYWPEKRGIYGKVEVLVISVNECDNYTIRNLVLKQGSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRLASQGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRMDRGGMVQTSEQYEFVHHALCLYESRLSAET 655
               SCOP domains d2              a8ba_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2a              8bA00 A:-1-655 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------------...eehhhhhhhh.hhhhhhhhhhh......hhhhh...hhhhhh.......hhh.eee.......hhhh.eeeeeee.hhhhh...eeee...hhhhhhhhhhhhhhhh..eeeee.................eeee..eeeeeeeeee....eeeeeeeee..eeeeeeeeee...........hhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------I----------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------TYR_PHOSPHATASE_PTP  PDB: A:393-647 UniProt: 393-647                                                                                                                                                                                                           -------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:562-638 UniProt: 562-638                           ----------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.8  PDB: A:-1-398 (gaps)          ----------------------------Exon 1.10  PDB: A:427-453  Exon 1.11  PDB: A:454-499 UniProt: 454-499    Exon 1.12  PDB: A:500-536            Exon 1.13  PDB: A:537-589 UniProt: 537-589           -------------------------------------Exon 1.15b  PDB: A:627-655    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.9  PDB: A:399-427     -----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:589-627              ---------------------------- Transcript 1 (2)
                 2a8b A  -1 IP--------------SRILTRSQLRDVVASSHLLQSEFMEIPMNFVDPKEIDIPRHGTKNRYKTILPNPLSRVCLRPKNVTDSLSTYINANYIRGYSGKEKAFIATQGPMINTVDDFWQMVWQEDSPVIVMITKLKEKNEKCVLYWPEKRGIYGKVEVLVISVNECDNYTIRNLVLKQGSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRLASQGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRMDRGGMVQTSEQYEFVHHALCLYESRLSAET 655
                             |       -      |378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       
                             0            375                                                                                                                                                                                                                                                                                        

   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 2A8B)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTPRR_HUMAN | Q15256)
molecular function
    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:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0010633    negative regulation of epithelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    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:1903385    regulation of homophilic cell adhesion    Any process that modulates the frequency, rate or extent of homophilic cell adhesion.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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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 Related Entries

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(-) Related Entries Specified in the PDB File

1jln CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE PHOSPHATASE PTP-SI/BR7