Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
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

Title :  CRYSTAL STRUCTURE OF THE TYROSINE PHOSPHATASE SHP-2 WITH Q506P MUTATION
 
Authors :  W. Qiu, A. Lin, A. Hutchinson, V. Romanov, M. Ruzanov, C. Thompson, K. La G. Kisselman, K. Battaile, N. Y. Chirgadze
Date :  13 Sep 12  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Proteins, Sh2 Domain, Phosphatase Domain, Tyrosine Phosphatase Shp-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Qiu, A. Lin, A. Hutchinson, V. Romanov, M. Ruzanov, C. Thompson, K. Lam, G. Kisselman, K. Battaile, N. Y. Chirgadze
Crystal Structure Of The Tyrosine Phosphatase Shp-2 With Q506P Mutation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-SH2, C-SH2 AND PHOSPHATASE DOMAIN
    Gene: PTPN11, PTP2C, SHPTP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE 1D, PTP-1D, PROTEIN-TYROSINE PHOSPHATASE 2C, PTP-2C, SH-PTP2, SHP-2, SHP2, SH-PTP3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ARG A:32 , LYS A:35 , MET A:311BINDING SITE FOR RESIDUE EDO A 601
2AC2SOFTWAREGLY A:39 , ASN A:58 , THR A:507 , GLU A:508BINDING SITE FOR RESIDUE EDO A 602
3AC3SOFTWAREASP A:431 , PRO A:432 , GLY A:434 , VAL A:435 , LYS A:534BINDING SITE FOR RESIDUE EDO A 603
4AC4SOFTWARECYS A:259 , LYS A:260 , LEU A:262BINDING SITE FOR RESIDUE GOL A 604
5AC5SOFTWAREASP A:64 , LEU A:65 , GLY A:67BINDING SITE FOR RESIDUE EDO A 605
6AC6SOFTWAREGLN A:57 , PHE A:346 , ASN A:349 , ARG A:413BINDING SITE FOR RESIDUE EDO A 606
7AC7SOFTWAREASN A:339 , ARG A:343 , TYR A:380 , GLY A:381 , VAL A:382BINDING SITE FOR RESIDUE EDO A 607
8AC8SOFTWAREGLU A:123 , HIS A:169BINDING SITE FOR RESIDUE GOL A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H34)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:85 -Gly A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H34)

(-) Exons   (0, 0)

(no "Exon" information available for 4H34)

(-) 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:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4h34a1 A:4-110 automated matches                                                                   d4h34a2 A:111-218 automated matches                                                              d4h34a3 A:219-537 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh....eeeeee.......eeeeeee..eeeeeeeee....eee....ee.hhhhhhhhhh..........ee...........eee..hhhhhhhhhhhh....eeeeee.......eeeeee...eeeeeeeee..eee........hhhhhhhhhhhh.ee.....ee...ee.....ee..hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....................eeee......eeee......hhhhhhhhhhhh...eeee...................eeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeee...........hhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h34 A   4 RRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHSDYINANIIMPEFKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVPTEAQYRFIYMAVQHYIETLQRRIEEEQKSKR 537
                                    13        23        33        43        53        63        73        83   ||  100       110       120       130       140       150  ||   171       181       191       201       211       221       231   ||  251       261       271       281       291 ||    309    || 329       339       349       359||     371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531      
                                                                                                              87|                                                       153|                                                                   235|                                            293|         314|                                360|                                                                                                                                                                              
                                                                                                               95                                                        165                                                                    246                                             302          325                                 363
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H34)

(-) Gene Ontology  (78, 78)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) 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)
    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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:85 - Gly A:86   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4h34
    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
  PTN11_HUMAN | Q06124
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  PTN11_HUMAN | Q06124
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PTN11_HUMAN | Q06124: 2shp 3b7o 3mow 3o5x 3tkz 3tl0 3zm0 3zm1 3zm2 3zm3 4dgp 4dgx 4gwf 4h1o 4je4 4jeg 4jmg 4nwf 4nwg 4ohd 4ohe 4ohh 4ohi 4ohl 4pvg 4qsy 4rdd 5df6 5ehp 5ehr 5i6v 5ibm 5ibs

(-) Related Entries Specified in the PDB File

4gwf THE SAME PROTEIN WITH Y279C MUTATION
4h1o THE SAME PROTEIN WITH D61G MUTATION