Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF SHH VARIANT OF "BERGERAC" CHIMERA OF SPECTRIN SH3
 
Authors :  A. G. Gabdoulkhakov, L. V. Gushchina, A. D. Nikulin, S. V. Nikonov, A. R. L. Serrano, V. V. Filimonov
Date :  18 Dec 06  (Deposition) - 08 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Sh3 Domain, Chimera, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. V. Gushchina, A. G. Gabdulkhakov, S. V. Nikonov, P. L. Mateo, V. V. Filimonov
Structural And Thermodynamic Studies Of Bergerac-Sh3 Chimeras.
Biophys. Chem. V. 139 106 2009
PubMed-ID: 19042078  |  Reference-DOI: 10.1016/J.BPC.2008.10.011

(-) Compounds

Molecule 1 - SPECTRIN ALPHA CHAIN, BRAIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAT-4/SHH
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: SPECTRIN, NON-ERYTHROID ALPHA CHAIN, FODRIN ALPHA CHAIN

 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
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:1049 , ASN A:1051 , GLY A:1052 , THR B:2049 , GLY B:2052BINDING SITE FOR RESIDUE CL B 5001
2AC2SOFTWARETHR C:3049 , GLY C:3052 , THR D:4049 , GLY D:4052BINDING SITE FOR RESIDUE CL D 5002
3AC3SOFTWAREASP A:1014 , HOH B:5044BINDING SITE FOR RESIDUE CL A 5005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OAW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OAW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OAW)

(-) Exons   (0, 0)

(no "Exon" information available for 2OAW)

(-) 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:65
 aligned with SPTN1_CHICK | P07751 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:65
                                                                  1010     1011              
                                   978       988       998      1008 |       -|     1020     
         SPTN1_CHICK    969 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVN--------DRQGFVPAAYVKKLD 1025
               SCOP domains d2oawa_ A: automated matches                                      SCOP domains
               CATH domains 2oawA00 A:1006-1070 SH3 Domains                                   CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeee.....eeeeeeeeee..eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                2oaw A 1006 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVKITVNGKTYERQGFVPAAYVKKLD 1070
                                  1015      1025      1035      1045      1055      1065     


Chain B from PDB  Type:PROTEIN  Length:65
 aligned with SPTN1_CHICK | P07751 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:65
                                                                  1010     1011              
                                   978       988       998      1008 |       -|     1020     
         SPTN1_CHICK    969 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVN--------DRQGFVPAAYVKKLD 1025
               SCOP domains d2oawb_ B: automated matches                                      SCOP domains
               CATH domains 2oawB00 B:2006-2070 SH3 Domains                                   CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeee.....eeeeeeeeee..eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                2oaw B 2006 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVKITVNGKTYERQGFVPAAYVKKLD 2070
                                  2015      2025      2035      2045      2055      2065     


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with SPTN1_CHICK | P07751 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:65
                                                                  1010     1011              
                                   978       988       998      1008 |       -|     1020     
         SPTN1_CHICK    969 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVN--------DRQGFVPAAYVKKLD 1025
               SCOP domains d2oawc_ C: automated matches                                      SCOP domains
               CATH domains 2oawC00 C:3006-3070 SH3 Domains                                   CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..................eeeeee.....eeeeeeeeee..eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                2oaw C 3006 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVKITVNGKTYERQGFVPAAYVKKLD 3070
                                  3015      3025      3035      3045      3055      3065     


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with SPTN1_CHICK | P07751 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:65
                                                                  1010     1011              
                                   978       988       998      1008 |       -|     1020     
         SPTN1_CHICK    969 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVN--------DRQGFVPAAYVKKLD 1025
               SCOP domains d2oawd_ D: automated matches                                      SCOP domains
               CATH domains 2oawD00 D:4006-4070 SH3 Domains                                   CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..................eeeeee.....eeeeeeeeee..eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                2oaw D 4006 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVKITVNGKTYERQGFVPAAYVKKLD 4070
                                  4015      4025      4035      4045      4055      4065
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Roll (1513)
(-)
Topology: SH3 type barrels. (648)
(-)
Homologous Superfamily: SH3 Domains (267)
(-)
Chicken (Gallus gallus) (32)
1a2oawA00A:1006-1070
1b2oawB00B:2006-2070
1c2oawC00C:3006-3070
1d2oawD00D:4006-4070

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OAW)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SPTN1_CHICK | P07751)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0051693    actin filament capping    The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

 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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oaw)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  2oaw
    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
  SPTN1_CHICK | P07751
    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
  SPTN1_CHICK | P07751
    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
        SPTN1_CHICK | P07751: 1aey 1aj3 1bk2 1cun 1e6g 1e6h 1e7o 1g2b 1h8k 1hd3 1m8m 1neg 1pwt 1qkw 1qkx 1shg 1tuc 1tud 1u06 1u4q 1u5p 1uue 2cdt 2f2v 2f2w 2f2x 2jm8 2jm9 2jma 2jmc 2kr3 2kxd 2lj3 2nuz 2rmo 2rot 3i9q 3m0p 3m0q 3m0r 3m0s 3m0t 3m0u 3ngp 4f16 4f17 5ihi 5ihk 5ihn 5m6s

(-) Related Entries Specified in the PDB File

1bk2 A SPECTRIN SH3 DOMAIN D48G MUTANT
1shg CRYSTAL STRUCTURE OF A SRC-HOMOLOGY 3 (SH3) DOMAIN