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

(-) Description

Title :  CRYSTAL STRUCTURE OF SRC SH2 DOMAIN BOUND TO DOUBLY PHOSPHORYLATED PEPTIDE PQPYEPYIPI
 
Authors :  O. Y. Lubman, G. Waksman
Date :  18 Feb 03  (Deposition) - 22 Apr 03  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Sh2 Domain, Phosphotyrosine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Y. Lubman, G. Waksman
Structural And Thermodynamic Basis For The Interaction Of The Src Sh2 Domain With The Activated Form Of The Pdgf Beta-Receptor
J. Mol. Biol. V. 328 655 2003
PubMed-ID: 12706723  |  Reference-DOI: 10.1016/S0022-2836(03)00344-9

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC
    ChainsA, B
    EC Number2.7.1.112
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET3
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GeneV-SRC
    Organism ScientificROUS SARCOMA VIRUS (STRAIN SCHMIDT-RUPPIN)
    Organism Taxid11889
    StrainSCHMIDT-RUPPIN
    SynonymP60-SRC
 
Molecule 2 - DOUBLY PHOSPHORYLATED PEPTIDE LIGAND (PQPYEPYIPI)
    ChainsC
    EngineeredYES
    SyntheticYES

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3PTR-1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:181 , CYS A:187BINDING SITE FOR RESIDUE CL A 2000
2AC2SOFTWAREPHE A:152 , GLU B:252BINDING SITE FOR RESIDUE PG4 A 3000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  2A:150-247
B:254-351
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  1A:150-247
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SRC_RSVSA148-245
 
  1-
B:254-351

(-) Exons   (0, 0)

(no "Exon" information available for 1NZL)

(-) 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:101
 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 d1nzla_ A: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1nzlA00 A:147-249 SHC Adaptor Prote  in                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh.......eeeeee...--..eeeeeeeee...eeeeeeeeeeee...eee........hhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: A:150-247 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1nzl A 147 AEEWYFGKITRRESERLLLNPENPRGTFLVRESET--GAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 249
                                   156       166       176    |  186       196       206       216       226       236       246   
                                                            181  |                                                                 
                                                               184                                                                 

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 d1nzlb_ B: c-src tyrosine kinase                                                                        SCOP domains
               CATH domains 1nzlB00 B:251-353 SHC Adaptor Protein                                                                   CATH domains
           Pfam domains (1) ---SH2-1nzlB01 B:254-336                                                              ----------------- Pfam domains (1)
           Pfam domains (2) ---SH2-1nzlB02 B:254-336                                                              ----------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhh.......eeeeee.......eeeeeeeee...eeeeeeeeeee.....eeee..eee.hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH2  PDB: B:254-351 UniProt: 148-245                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1nzl B 251 AEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPT 353
                                   260       270       280       290       300       310       320       330       340       350   

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1nzl C 498 PQyEyIPA 505
                              | |   
                            500-PTR 
                              502-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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) 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.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nzl)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1nzl
    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
  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)
  2.7.1.112
    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
  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
        SRC_RSVSA | P005241bkl 1bkm 1is0 1kc2 1nzv 1sha 1shb 1skj 1spr 1sps

(-) Related Entries Specified in the PDB File

1is0 1kc2