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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PTP10D FROM DROSOPHILA MELANOGASTER WITH A SMALL MOLECULE INHIBITOR VANADATE
 
Authors :  L. L. Madan, B. Gopal
Date :  18 May 11  (Deposition) - 02 Nov 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Differentiation, Neurogenesis, Signal Transduction, Developmental Protein, Hydrolase, Protein Phosphatase, Protein Tyrosine Phosphatase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. L. Madan, B. Gopal
Conformational Basis For Substrate Recruitment In Protein Tyrosine Phosphatase 10D
Biochemistry V. 50 10114 2011
PubMed-ID: 22007620  |  Reference-DOI: 10.1021/BI201092Q

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE 10D
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1250-1533
    GeneCG1817, PTP10D
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymRECEPTOR-LINKED PROTEIN-TYROSINE PHOSPHATASE 10D, DPTP10D

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
11BO2Ligand/Ion1-BUTANOL
2BU11Ligand/Ion1,4-BUTANEDIOL
3IPA2Ligand/IonISOPROPYL ALCOHOL
4VO41Ligand/IonVANADATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
11BO1Ligand/Ion1-BUTANOL
2BU1-1Ligand/Ion1,4-BUTANEDIOL
3IPA2Ligand/IonISOPROPYL ALCOHOL
4VO4-1Ligand/IonVANADATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
11BO1Ligand/Ion1-BUTANOL
2BU11Ligand/Ion1,4-BUTANEDIOL
3IPA-1Ligand/IonISOPROPYL ALCOHOL
4VO41Ligand/IonVANADATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:20BINDING SITE FOR RESIDUE 1BO A 308
2AC2SOFTWARELEU A:80BINDING SITE FOR RESIDUE IPA A 309
3AC3SOFTWAREASP A:178 , SER A:179 , HIS A:180BINDING SITE FOR RESIDUE IPA A 310
4AC4SOFTWARELYS B:154 , SER B:243 , ALA B:244BINDING SITE FOR RESIDUE VO4 B 308
5AC5SOFTWAREGLY B:108 , ASN B:110 , SER B:111 , PRO B:112BINDING SITE FOR RESIDUE BU1 B 309
6AC6SOFTWAREILE B:262 , ASN B:263BINDING SITE FOR RESIDUE 1BO B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S3F)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:215 -Pro A:216
2Arg B:236 -Pro B:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S3F)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTP10_DROME1272-1527
 
  2A:46-301
B:46-301
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTP10_DROME1444-1518
 
  2A:218-292
B:218-292
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTP10_DROME1466-1476
 
  2A:240-250
B:240-250
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTP10_DROME1272-1527
 
  1A:46-301
-
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTP10_DROME1444-1518
 
  1A:218-292
-
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTP10_DROME1466-1476
 
  1A:240-250
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTP10_DROME1272-1527
 
  1-
B:46-301
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTP10_DROME1444-1518
 
  1-
B:218-292
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTP10_DROME1466-1476
 
  1-
B:240-250

(-) Exons   (0, 0)

(no "Exon" information available for 3S3F)

(-) Sequences/Alignments

Asymmetric 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:287
 aligned with PTP10_DROME | P35992 from UniProtKB/Swiss-Prot  Length:1990

    Alignment length:295
                                  1246      1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526     
         PTP10_DROME   1237 DNMSLPDSVIEQNRPILIKNFAEHYRLMSADSDFRFSEEFEELKHVGRDQPCTFADLPCNRPKNRFTNILPYDHSRFKLQPVDDDEGSDYINANYVPGHNSPREFIVTQGPLHSTRDDFWRMCWESNSRAIVMLTRCFEKGREKCDQYWPNDTVPVFYGDIKVQILNDSHYADWVMTEFMLCRGSEQRILRHFHFTTWPDFGVPNPPQTLVRFVRAFRDRIGAEQRPIVVHCSAGVGRSGTFITLDRILQQINTSDYVDIFGIVYAMRKERVWMVQTEQQYICIHQCLLAVLEGK 1531
               SCOP domains d3s3f        a_ A: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--------..ee..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhh............................eeee........eeee...hhhhhhhhhhhhhhhh..eeee....ee..ee............eee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee...........hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------TYR_PHOSPHATASE_PTP  PDB: A:46-301 UniProt: 1272-1527                                                                                                                                                                                                           ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:218-292 UniProt: 1444-1518                       ------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3s3f A   19 SHMAS--------RPILIKNFAEHYRLMSADSDFRFSEEFEELKHVGRDQPCTFADLPCNRPKNRFTNILPYDHSRFKLQPVDDDEGSDYINANYVPGHNSPREFIVTQGPLHSTRDDFWRMCWESNSRAIVMLTRCFEKGREKCDQYWPNDTVPVFYGDIKVQILNDSHYADWVMTEFMLCRGSEQRILRHFHFTTWPDFGVPNPPQTLVRFVRAFRDRIGAEQRPIVVHCSAGVGRSGTFITLDRILQQINTSDYVDIFGIVYAMRKERVWMVQTEQQYICIHQCLLAVLEGK  305
                                |    -   |    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
                               23       24                                                                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with PTP10_DROME | P35992 from UniProtKB/Swiss-Prot  Length:1990

    Alignment length:285
                                  1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526     
         PTP10_DROME   1247 EQNRPILIKNFAEHYRLMSADSDFRFSEEFEELKHVGRDQPCTFADLPCNRPKNRFTNILPYDHSRFKLQPVDDDEGSDYINANYVPGHNSPREFIVTQGPLHSTRDDFWRMCWESNSRAIVMLTRCFEKGREKCDQYWPNDTVPVFYGDIKVQILNDSHYADWVMTEFMLCRGSEQRILRHFHFTTWPDFGVPNPPQTLVRFVRAFRDRIGAEQRPIVVHCSAGVGRSGTFITLDRILQQINTSDYVDIFGIVYAMRKERVWMVQTEQQYICIHQCLLAVLEGK 1531
               SCOP domains d3s3fb_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.......hhh.eee...........eeeeeee........eeee...hhhhhhhhhhhhhhh...eeee....ee..ee............eee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee...........hhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh....eehhhhhhhhhhh.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_PTP  PDB: B:46-301 UniProt: 1272-1527                                                                                                                                                                                                           ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:218-292 UniProt: 1444-1518                       ------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3s3f B   21 MASRPILIKNFAEHYRLMSADSDFRFSEEFEELKHVGRDQPCTFADLPCNRPKNRFTNILPYDHSRFKLQPVDDDEGSDYINANYVPGHNSPREFIVTQGPLHSTRDDFWRMCWESNSRAIVMLTRCFEKGREKCDQYWPNDTVPVFYGDIKVQILNDSHYADWVMTEFMLCRGSEQRILRHFHFTTWPDFGVPNPPQTLVRFVRAFRDRIGAEQRPIVVHCSAGVGRSGTFITLDRILQQINTSDYVDIFGIVYAMRKERVWMVQTEQQYICIHQCLLAVLEGK  305
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S3F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S3F)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PTP10_DROME | P35992)
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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0004728    signal transducer, downstream of receptor, with protein tyrosine phosphatase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by 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: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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0007424    open tracheal system development    The process whose specific outcome is the progression of an open tracheal system over time, from its formation to the mature structure. An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
    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:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    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: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: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

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

UniProtKB/Swiss-Prot
        PTP10_DROME | P359923s3e 3s3h 3s3k

(-) Related Entries Specified in the PDB File

3s3e 3s3h 3s3k