Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PROTEIN TYROSINE PHOSPHATASE (PUTATIVE) FROM LEISHMANIA MAJOR
 
Authors :  E. A. Merritt, T. Arakaki, Medical Structural Genomics Of Pathoge Protozoa (Msgpp), Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)
Date :  19 May 11  (Deposition) - 15 Jun 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Merritt, T. Arakaki, H. Neely, E. Phizicky, E. Quartley, W. C. Van Voorhis, F. S. Buckner, E. Fan, F. Zucker, C. L. M. J. Verlinde W. G. J. Hol
Protein Tyrosine Phosphatase From Leishmania Major
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE-LIKE PROTEIN
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 4-167
    Gene: LMJF16.0230, LMJF_16_0230
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: FRIEDLIN

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE
3THJ1Ligand/IonTHIOSULFATE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
3THJ1Ligand/IonTHIOSULFATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
3THJ-1Ligand/IonTHIOSULFATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:74 , CYS A:112 , VAL A:113 , ALA A:114 , GLY A:115 , LEU A:116 , GLY A:117 , ARG A:118 , ALA A:119BINDING SITE FOR RESIDUE THJ A 170
2AC2SOFTWAREHIS A:41 , ARG A:42 , GLY A:43 , ARG A:45 , ARG A:96 , PRO A:104 , PRO A:105 , PRO A:106 , THR A:107 , HOH A:190 , HOH A:193 , HOH A:202 , HIS B:41 , ARG B:42 , GLY B:43 , ARG B:45 , ARG B:96 , PRO B:105 , PRO B:106 , THR B:107BINDING SITE FOR RESIDUE EPE A 164

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:51 -A:112
2B:51 -B:112

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S4O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S4O)

(-) Exons   (0, 0)

(no "Exon" information available for 3S4O)

(-) 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:163
 aligned with Q4QEZ7_LEIMA | Q4QEZ7 from UniProtKB/TrEMBL  Length:175

    Alignment length:163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   
         Q4QEZ7_LEIMA     3 VNATLIDCCDPQKPSRVLFHFLILDAPSPSNLPTYIKELQHRGVRHLVRVCGPTYDATLVKSRGIDVHSWPFDDGAPPTRAVLDSWLKLLDTELARQQEDPSVPPPTIGVHCVAGLGRAPILVALALVEYGNVSALDAIALIREKRKGAINQTQMHWITKYKR 165
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s4o A   1 mNATLIDCCDPQKPSRVLFHFLILDAPSPSNLPTYIKELQHRGVRHLVRVCGPTYDATLVKSRGIDVHSWPFDDGAPPTRAVLDSWLKLLDTELARQQEDPSVPPPTIGVHCVAGLGRAPILVALALVEYGNVSALDAIALIREKRKGAINQTQmHWITKYKR 163
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    |  160   
                            |                                                                                                                                                       155-MSE    
                            1-MSE                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with Q4QEZ7_LEIMA | Q4QEZ7 from UniProtKB/TrEMBL  Length:175

    Alignment length:163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   
         Q4QEZ7_LEIMA     3 VNATLIDCCDPQKPSRVLFHFLILDAPSPSNLPTYIKELQHRGVRHLVRVCGPTYDATLVKSRGIDVHSWPFDDGAPPTRAVLDSWLKLLDTELARQQEDPSVPPPTIGVHCVAGLGRAPILVALALVEYGNVSALDAIALIREKRKGAINQTQMHWITKYKR 165
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------DSPc-3s4oB01 B:88-163                                                        Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------DSPc-3s4oB02 B:88-163                                                        Pfam domains (2)
         Sec.struct. author ...eeeeee.......eeeeeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s4o B   1 mNATLIDCCDPQKPSRVLFHFLILDAPSPSNLPTYIKELQHRGVRHLVRVCGPTYDATLVKSRGIDVHSWPFDDGAPPTRAVLDSWLKLLDTELARQQEDPSVPPPTIGVHCVAGLGRAPILVALALVEYGNVSALDAIALIREKRKGAINQTQmHWITKYKR 163
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    |  160   
                            1-MSE                                                                                                                                                   155-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3S4O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S4O)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Phosphatase (121)
(-)
Family: DSPc (22)
(-)
Leishmania major (1)
1aDSPc-3s4oB01B:88-163
1bDSPc-3s4oB02B:88-163

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4QEZ7_LEIMA | Q4QEZ7)
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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and 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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric 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)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    THJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3s4o)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3s4o
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q4QEZ7_LEIMA | Q4QEZ7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.48
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q4QEZ7_LEIMA | Q4QEZ7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3S4O)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3S4O)