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

(-) Description

Title :  A-SPECTRIN SH3 DOMAIN F52Y MUTANT
 
Authors :  M. C. Vega, A. R. Viguera, L. Serrano
Date :  06 Nov 00  (Deposition) - 01 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Sh3-Domain, Cytoskeleton, Calmodulin-Binding, Actin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Viguera, C. Vega, L. Serrano
Unspecific Hydrophobic Stabilization Of Folding Transition States
Proc. Natl. Acad. Sci. Usa V. 99 5349 2002
PubMed-ID: 11959988  |  Reference-DOI: 10.1073/PNAS.072387799
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPECTRIN ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR322
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PBAT4
    Fragment: SH3-DOMAIN RESIDUES 964-1025
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Plasmid: PBR322
    Strain: BL21(DE3)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:42 , LYS A:60BINDING SITE FOR RESIDUE SO4 A 161
2AC2SOFTWARETYR A:13 , TRP A:41 , HOH A:2002 , HOH A:2056BINDING SITE FOR RESIDUE GOL A 162
3AC3SOFTWAREGLN A:16 , GLU A:17 , ASP A:40 , PRO A:54 , ALA A:55 , ALA A:56 , HOH A:2022 , HOH A:2057 , HOH A:2058BINDING SITE FOR RESIDUE GOL A 163

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HD3)

(-) Exons   (0, 0)

(no "Exon" information available for 1HD3)

(-) Sequences/Alignments

Asymmetric/Biological 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:58
 aligned with SPTN1_CHICK | P07751 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:58
                                   977       987       997      1007      1017        
         SPTN1_CHICK    968 GKELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD 1025
               SCOP domains d1hd3a_ A: alpha-Spectrin, SH3 domain                      SCOP domains
               CATH domains 1hd3A00 A:5-62 SH3 Domains                                 CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeeeee.....eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                1hd3 A    5 GKELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGYVPAAYVKKLD   62
                                    14        24        34        44        54
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HD3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 1hd3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1hd3
    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 1m8m 1neg 1pwt 1qkw 1qkx 1shg 1tuc 1tud 1u06 1u4q 1u5p 1uue 2cdt 2f2v 2f2w 2f2x 2jm8 2jm9 2jma 2jmc 2kr3 2kxd 2lj3 2nuz 2oaw 2rmo 2rot 3i9q 3m0p 3m0q 3m0r 3m0s 3m0t 3m0u 3ngp 4f16 4f17 5ihi 5ihk 5ihn 5m6s

(-) Related Entries Specified in the PDB File

1aey ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, SOLUTION NMR, 15 STRUCTURES
1aj3 SOLUTION STRUCTURE OF THE SPECTRIN REPEAT, NMR, 20 STRUCTURES
1bk2 A-SPECTRIN SH3 DOMAIN D48G MUTANT
1cun CRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA SPECTRIN
1e6g A-SPECTRIN SH3 DOMAIN D48G MUTANT
1e6h A-SPECTRIN SH3 DOMAIN A11V, M25I, V44I, V58L MUTANTS
1e7o A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V44I, V58L MUTATIONS
1pwt THERMODYNAMIC ANALYSIS OF ALPHA-SPECTRIN SH3 AND TWO OF ITSCIRCULAR PERMUTANTS WITH DIFFERENT LOOP LENGTHS: DISCERNINGTHE REASONS FOR RAPID FOLDING IN PROTEINS
1qkw ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, N47G MUTANT IN THE DISTAL LOOP
1qkx ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, N47A MUTANT IN THE DISTAL LOOP.
1shg ALPHA SPECTRIN (SH3 DOMAIN), GALLUS GALLUS BRAIN
1tuc ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT S19-P20
1tud ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47-D48