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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX OF THE SRC SH2 DOMAIN WITH CONFORMATIONALLY CONSTRAINED PEPTIDE INHIBITOR
 
Authors :  J. P. Davidson, O. Lubman, T. Rose, G. Waksman, S. F. Martin
Date :  02 Nov 01  (Deposition) - 06 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Conformationaly Constrained Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Davidson, O. Lubman, T. Rose, G. Waksman, S. F. Martin
Calorimetric And Structural Studies Of 1, 2, 3-Trisubstituted Cyclopropanes As Conformationally Constrained Peptide Inhibitors Of Src Sh2 Domain Binding.
J. Am. Chem. Soc. V. 124 205 2002
PubMed-ID: 11782172  |  Reference-DOI: 10.1021/JA011746F

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC
    ChainsA, B
    EC Number2.7.1.112
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    Organism ScientificROUS SARCOMA VIRUS
    Organism Taxid11886
    SynonymSRC
 
Molecule 2 - AY0 GLU GLU ILE PEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AY02Mod. Amino Acid(1R,2R,3S)-2-(METHYLCARBAMOYL)-3-[4-(PHOSPHONOOXY)PHENYL]CYCLOPROPANECARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AY01Mod. Amino Acid(1R,2R,3S)-2-(METHYLCARBAMOYL)-3-[4-(PHOSPHONOOXY)PHENYL]CYCLOPROPANECARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AY01Mod. Amino Acid(1R,2R,3S)-2-(METHYLCARBAMOYL)-3-[4-(PHOSPHONOOXY)PHENYL]CYCLOPROPANECARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:155 , ARG A:175 , SER A:177 , GLU A:178 , THR A:179 , CYS A:185 , LYS A:200 , HIS A:201 , TYR A:202 , LYS A:203 , ILE A:214 , THR A:215 , TYR A:230 , ASP A:235 , GLY A:236 , LEU A:237 , HOH A:1029 , ARG B:205 , HOH C:1010 , HOH C:1035 , AY0 D:352 , GLU D:354BINDING SITE FOR CHAIN C OF AY0 GLU GLU ILE PEPTIDE
2AC2SOFTWAREARG A:155 , ARG A:156 , GLU A:178 , THR A:179 , LYS B:152 , ARG B:155 , ARG B:175 , SER B:177 , GLU B:178 , THR B:179 , CYS B:185 , LYS B:200 , HIS B:201 , TYR B:202 , LYS B:203 , ARG B:205 , THR B:215 , HOH B:1081 , HOH B:1124 , AY0 C:252 , HOH D:1022 , HOH D:1031 , HOH D:1043 , HOH D:1056 , HOH D:1121BINDING SITE FOR CHAIN D OF AY0 GLU GLU ILE PEPTIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IS0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IS0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  2A:148-245
B:148-245
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  1A:148-245
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  1-
B:148-245

(-) Exons   (0, 0)

(no "Exon" information available for 1IS0)

(-) 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:102
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:102
                                   155       165       175       185       195       205       215       225       235       245  
            SRC_RSVSA   146 EEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1is0a_ A: c-src tyrosine kinase                                                                       SCOP domains
               CATH domains 1is0A00 A:146-247 SHC Adaptor Protein                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....ee.....ee.hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --SH2  PDB: A:148-245 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1is0 A 146 EEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
                                   155       165       175       185       195       205       215       225       235       245  

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with SRC_RSVSA | P00524 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:102
                                   155       165       175       185       195       205       215       225       235       245  
            SRC_RSVSA   146 EEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
               SCOP domains d1is0b_ B: c-src tyrosine kinase                                                                       SCOP domains
               CATH domains 1is0B00 B:146-247 SHC Adaptor Protein                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....ee.....ee.hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --SH2  PDB: B:148-245 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1is0 B 146 EEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 247
                                   155       165       175       185       195       205       215       225       235       245  

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
                 1is0 C 252 xEEI 255
                            |   
                          252-AY0

Chain D 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
                 1is0 D 352 xEEI 355
                            |   
                            |   
                          352-AY0

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IS0)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1kc2 1nzl 1nzv 1sha 1shb 1skj 1spr 1sps

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