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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS
 
Authors :  G. Waksman, J. Kuriyan
Date :  05 Mar 93  (Deposition) - 31 May 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Transferase(Phosphotransferase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Waksman, S. E. Shoelson, N. Pant, D. Cowburn, J. Kuriyan
Binding Of A High Affinity Phosphotyrosyl Peptide To The Src Sh2 Domain: Crystal Structures Of The Complexed And Peptide-Free Forms.
Cell(Cambridge, Mass. ) V. 72 779 1993
PubMed-ID: 7680960  |  Reference-DOI: 10.1016/0092-8674(93)90405-F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SRC SH2 DOMAIN
    ChainsA, B, C
    EngineeredYES
    Organism ScientificROUS SARCOMA VIRUS
    Organism Taxid11886
 
Molecule 2 - PEPTIDE YEEI
    ChainsD, E, F
    EngineeredYES
    Organism ScientificHAMSTER POLYOMAVIRUS
    Organism Taxid10626

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A  D  
Biological Unit 2 (1x) B  E 
Biological Unit 3 (1x)  C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PTR3Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 1SPS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SPS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SPS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SPS)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
  3A:5-102
B:5-102
C:5-102
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
  1A:5-102
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
  1-
B:5-102
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
  1-
-
C:5-102

(-) Exons   (0, 0)

(no "Exon" information available for 1SPS)

(-) 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:103
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:103
                                   154       164       174       184       194       204       214       224       234       244   
            SRC_RSVSA   145 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1spsa_ A: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1spsA00 A:2-104 SHC Adaptor Protein                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....ee........hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: A:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1sps A   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:103
                                   154       164       174       184       194       204       214       224       234       244   
            SRC_RSVSA   145 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1spsb_ B: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1spsB00 B:2-104 SHC Adaptor Protein                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh........eeeee.......eeeeeeee.....eeeeeeeeee.....ee.....ee.hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: B:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1sps B   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:103
                                   154       164       174       184       194       204       214       224       234       244   
            SRC_RSVSA   145 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1spsc_ C: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1spsC00 C:2-104 SHC Adaptor Protein                                                                     CATH domains
           Pfam domains (1) ---SH2-1spsC01 C:5-87                                                                 ----------------- Pfam domains (1)
           Pfam domains (2) ---SH2-1spsC02 C:5-87                                                                 ----------------- Pfam domains (2)
           Pfam domains (3) ---SH2-1spsC03 C:5-87                                                                 ----------------- Pfam domains (3)
         Sec.struct. author ....................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: C:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1sps C   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with MT_POVHA | P03079 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:7
             MT_POVHA   322 PQYEEIP 328
               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
                 1sps D  -2 PQyEEIP   4
                              |    
                              |    
                              0-PTR

Chain E from PDB  Type:PROTEIN  Length:6
 aligned with MT_POVHA | P03079 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:6
             MT_POVHA   322 PQYEEI 327
               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
                 1sps E  -2 PQyEEI   3
                              |   
                              0-PTR

Chain F from PDB  Type:PROTEIN  Length:10
 aligned with MT_POVHA | P03079 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:10
                                   331
             MT_POVHA   322 PQYEEIPIYL 331
               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
                 1sps F  -2 PQyEEIPIYL   7
                              |      7
                              0-PTR   

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SRC_RSVSA | P00524)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

Chain D,E,F   (MT_POVHA | P03079)
biological process
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.

 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
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1sps)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sps)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1sps
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MT_POVHA | P03079
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SRC_RSVSA | P00524
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MT_POVHA | P03079
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SRC_RSVSA | P00524
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MT_POVHA | P030791aot 1aou 1lcj 4u1p
        SRC_RSVSA | P005241bkl 1bkm 1is0 1kc2 1nzl 1nzv 1sha 1shb 1skj 1spr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SPS)