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(-) 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 :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (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 TYROSINE KINASE SH2 DOMAIN
    ChainsA, B, C, D
    EngineeredYES
    Organism ScientificROUS SARCOMA VIRUS
    Organism Taxid11886

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , ARG A:32 , SER A:34 , GLU A:35 , THR A:36 , CYS A:42 , LYS A:60 , GLN C:82 , HOH C:1053 , HOH C:1106BINDING SITE FOR RESIDUE PO4 A 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
 
  4A:5-102
B:5-102
C:5-102
D: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
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
 
 
  1-
-
-
D:5-102

(-) Exons   (0, 0)

(no "Exon" information available for 1SPR)

(-) 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 d1spra_ A: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1sprA00 A:2-104 SHC Adaptor Protein                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh........eeeee.......eeeeeeeee...eeeeeeeeeee.....ee.....ee.hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: A:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1spr A   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:104
                                   153       163       173       183       193       203       213       223       233       243    
            SRC_RSVSA   144 QAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1sprb_ B: c-src tyrosine kinase                                                                         SCOP domains
               CATH domains 1sprB00 B:1-104 SHC Adaptor Protein                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh........eeeee.......eeeeeeeee...eeeeeeeeeee.....ee........hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SH2  PDB: B:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1spr B   1 QAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    10        20        30        40        50        60        70        80        90       100    

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 d1sprc_ C: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1sprC00 C:2-104 SHC Adaptor Protein                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....ee........hhhhhhhhh............ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: C:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1spr C   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

Chain D 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 d1sprd_ D: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1sprD00 D:2-104 SHC Adaptor Protein                                                                     CATH domains
           Pfam domains (1) ---SH2-1sprD01 D:5-87                                                                 ----------------- Pfam domains (1)
           Pfam domains (2) ---SH2-1sprD02 D:5-87                                                                 ----------------- Pfam domains (2)
           Pfam domains (3) ---SH2-1sprD03 D:5-87                                                                 ----------------- Pfam domains (3)
           Pfam domains (4) ---SH2-1sprD04 D:5-87                                                                 ----------------- Pfam domains (4)
         Sec.struct. author .........hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....ee........hhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: D:5-102 UniProt: 148-245                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1spr D   2 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 104
                                    11        21        31        41        51        61        71        81        91       101   

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SRC_RSVSA | P005241bkl 1bkm 1is0 1kc2 1nzl 1nzv 1sha 1shb 1skj 1sps

(-) Related Entries Specified in the PDB File

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