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 PTPN11 TANDEM SH2 DOMAINS IN COMPLEX WITH A TXNIP PEPTIDE
 
Authors :  A. Dong, W. Li, W. Tempel, Y. Liu, C. Bountra, C. H. Arrowsmith, A. M. Edwa J. Min, Structural Genomics Consortium (Sgc)
Date :  26 Aug 15  (Deposition) - 23 Sep 15  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, J. Lau, W. Li, W. Tempel, L. Li, A. Dong, A. Narula, S. Qin, J. Min
Structural Basis For The Regulatory Role Of The Ppxy Motifs In The Thioredoxin-Interacting Protein Txnip.
Biochem. J. V. 473 179 2016
PubMed-ID: 26527736  |  Reference-DOI: 10.1042/BJ20150830

(-) 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 Plasmid: PET28-SACB-AP
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Gene: PTPN11, PTP2C, SHPTP2
    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,SHP2,SH-PTP3
 
Molecule 2 - TXNIP
    Chains: B, C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1NH22Mod. Amino AcidAMINO GROUP
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3UNX7Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:32 , SER A:34 , LYS A:35 , SER A:36 , THR A:42 , THR A:52 , HIS A:53 , GLU A:90 , THR B:377 , GLU B:380 , HOH B:501 , HOH B:502 , HOH B:503 , HOH B:504 , HOH B:505binding site for Ligand residues PTR B 378 through THR B 379 bound to THR B 377
2AC2SOFTWAREARG A:138 , SER A:140 , GLN A:141 , SER A:142 , VAL A:148 , THR A:168 , HIS A:169 , MET A:171 , THR C:377 , GLU C:380 , HOH C:501 , HOH C:502 , HOH C:503 , HOH C:504 , HOH C:507 , HOH C:511 , HOH C:512 , HOH C:514binding site for Ligand residues PTR C 378 through THR C 379 bound to THR C 377

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DF6)

(-) Exons   (0, 0)

(no "Exon" information available for 5DF6)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...eeeeee.......eeeeeee..eeeeeeeee....ee........hhhhhhhhhhhh....ee.........ee................hhhhhhhhhhhhh...eeeeee.......eeeeee...........eeeeee..............hhhhhhhhhhhh.ee.....ee...ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5df6 A   4 RRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESKSKVTHVMIRCQKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR 220
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153      |166       178       188       198       208       218  
                                                                                                                                                                                      160|        175|                                          
                                                                                                                                                                                       164         178                                          


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5df6 B 377 TxTEVDx 383
                             |    |
                           378-PTR|
                                383-NH2


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5df6 C 371 KFMPPPTxTEVDx 383
                                   380  |
                                 378-PTR|
                                      383-NH2
   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 5DF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DF6)

(-) Gene Ontology  (100, 105)

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
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5df6)
 

(-) 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
  5df6
    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
  TXNIP_HUMAN | Q9H3M7
    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)
  TXNIP_HUMAN | Q9H3M7
    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 4h34 4je4 4jeg 4jmg 4nwf 4nwg 4ohd 4ohe 4ohh 4ohi 4ohl 4pvg 4qsy 4rdd 5ehp 5ehr 5i6v 5ibm 5ibs
        TXNIP_HUMAN | Q9H3M7: 4gei 4gej 4gfx 4ll1 4ll4 4rof 4roj 5cq2 5dws 5dzd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DF6)