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 THE SECOND SH3 DOMAIN OF ITSN1 BOUND WITH A SYNTHETIC PEPTIDE
 
Authors :  A. Dong, X. Guan, H. Huang, A. Wernimont, J. Gu, S. Sidhu, C. Bountra, C. H. Arrowsmith, A. M. Edwards, Y. Tong, Structural Genomics Conso (Sgc)
Date :  20 Dec 12  (Deposition) - 23 Jan 13  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x),E (1x)
Keywords :  Sh3 Domain, Itsn1, Structural Genomics Consortium, Sgc, Protein- Peptide Complex, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Guan, A. Dong, H. Huang, A. Wernimont, J. Gu, S. Sidhu, C. Bountra, C. H. Arrowsmith, A. M. Edwards, Y. Tong, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Second Sh3 Domain Of Itsn1 Bound With A Synthetic Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERSECTIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHH0239
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ITSN1, ITSN, SH3D1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SH3 DOMAIN-CONTAINING PROTEIN 1A, SH3P17
 
Molecule 2 - PEPTIDE LIGAND
    Chains: C, D, E
    Engineered: YES
    Other Details: SYNTHETIC SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCDE
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1UNX11Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1UNX11Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNX-1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 4IIM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IIM)

(-) 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:57
                                                                                          
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee...eeeeee..eeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                4iim A  915 LLQAQALYPWRAKKDNHLNFNKNDVITVLEQQDMWWFGEVQGQKGWFPKSYVKLISA  971
                                   924       934       944       954       964       


Chain B from PDB  Type:PROTEIN  Length:55
                                                                                        
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee...eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                4iim B  915 LLQAQALYPWRAKKDNHLNFNKNDVITVLEQQDMWWFGEVQGQKGWFPKSYVKLI  969
                                   924       934       944       954       964     


Chain C from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                4iim C 2001 WRDSSGYVMGPW 2012
                                  2010  


Chain D from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                4iim D 2001 WRDSSGYVMGPW 2012
                                  2010  


Chain E from PDB  Type:PROTEIN  Length:5
                                      
               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
                4iim E 2011 VMGPW 2015
   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 4IIM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

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
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4iim)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4iim)
 
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
  4iim
    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
  ITSN1_HUMAN | Q15811
    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)
  (no 'Enzyme Classificator' available)
    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
  ITSN1_HUMAN | Q15811
    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
        ITSN1_HUMAN | Q15811: 1ki1 2kgr 2khn 3fia 3qbv 5hzi 5hzj 5hzk

(-) Related Entries Specified in the PDB File

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