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

(-) Description

Title :  CRYSTAL STRUCTURE OF SHP1 CATALYTIC DOMAIN WITH JAK1 ACTIVATION LOOP PEPTIDE
 
Authors :  N. L. Alicea-Velazquez, J. Jakoncic, T. J. Boggon
Date :  27 Aug 12  (Deposition) - 19 Dec 12  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Protein-Protein Complex, Phosphatase Domain, Hydrolase, Hydrolase- Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. L. Alicea-Velazquez, J. Jakoncic, T. J. Boggon
Structure-Guided Studies Of The Shp-1/Jak1 Interaction Provide New Insights Into Phosphatase Catalytic Domain Substrate Recognition.
J. Struct. Biol. V. 181 243 2013
PubMed-ID: 23296072  |  Reference-DOI: 10.1016/J.JSB.2012.12.009

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 6
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PHOSPHATASE DOMAIN (UNP RESIDUES 242-528)
    Gene: HCP, PTP1C, PTPN6, SHP-1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE, PROTEIN- TYROSINE PHOSPHATASE 1C, PTP-1C, PROTEIN-TYROSINE PHOSPHATASE SHP-1, SH-PTP1
 
Molecule 2 - TYROSINE-PROTEIN KINASE JAK1
    Chains: C
    EC Number: 2.7.10.2
    Engineered: YES
    Fragment: JAK1 ACTIVATION LOOP PHOPHOMIMETIC (UNP RESIDUES 1032- 1037)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JANUS KINASE 1, JAK-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FTY1Mod. Amino AcidDEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2UNK3Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FTY-1Mod. Amino AcidDEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2UNK-1Mod. Amino Acid
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FTY1Mod. Amino AcidDEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 4GS0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GS0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GS0)

(-) Exons   (0, 0)

(no "Exon" information available for 4GS0)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhh.................eeee.......eeee...hhhhhhhhhhhhhhhh..eeee....ee..ee...........eeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeee...........hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gs0 A 243 GFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQ 527
                                   252       262       272       282       292       302       312|      328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518         
                                                                                               312|                                                                                                                                                                                                                
                                                                                                319                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.......hhh.eee............eeeeeee.......eeee...hhhhhhhhhhhhhhhh..eeee....ee..ee...........eeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeee...........hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gs0 B 260 HQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKL 523
                                   269       279       289       299       309  ||   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515        
                                                                              312|                                                                                                                                                                                                            
                                                                               319                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4gs0 C   1 xxyx   4
                            ||||
                            1-UNK
                             2-UNK
                              3-FTY
                               4-UNK
   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 4GS0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GS0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GS0)

(-) Gene Ontology  (87, 95)

Asymmetric Unit(hide GO term definitions)

 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
    FTY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4gs0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gs0)
 
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 | Biol. Unit 1 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
  4gs0
    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
  JAK1_HUMAN | P23458
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PTN6_HUMAN | P29350
    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)
  2.7.10.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  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
  JAK1_HUMAN | P23458
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PTN6_HUMAN | P29350
    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
        JAK1_HUMAN | P23458: 3eyg 3eyh 4e4l 4e4n 4e5w 4ehz 4ei4 4fk6 4i5c 4ivb 4ivc 4ivd 4k6z 4k77 4l00 4l01 5e1e 5hx8 5ixd 5ixi 5khw 5khx 5l04
        PTN6_HUMAN | P29350: 1fpr 1gwz 1x6c 2b3o 2rmx 2yu7 3ps5 4gry 4grz 4hjp 4hjq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GS0)