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
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)

(-) Description

Title :  STRUCTURE OF A C2 DOMAIN
 
Authors :  D. A. K. Traore, J. C. Whisstock
Date :  24 Jan 13  (Deposition) - 23 Oct 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  C2 Domain, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Traore, A. J. Brennan, R. H. Law, C. Dogovski, M. A. Perugini, N. Lukoyanova, E. W. Leung, R. S. Norton, J. A. Lopez, K. A. Browne, H. Yagita, G. J. Lloyd, A. Ciccone, S. Verschoor, J. A. Trapani, J. C. Whisstock, I. Voskoboinik
Defining The Interaction Of Perforin With Calcium And The Phospholipid Membrane.
Biochem. J. V. 456 323 2013
PubMed-ID: 24070258  |  Reference-DOI: 10.1042/BJ20130999

(-) Compounds

Molecule 1 - C2 DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: SHUFFLE
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-129
    Gene: C2P1
    Organism Common: TURBOT
    Organism Scientific: SCOPHTHALMUS MAXIMUS
    Organism Taxid: 52904
    Synonym: SMC2P1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:35 , ASP A:41 , ASP A:88 , GLU A:89 , ASP A:90 , HOH A:325BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP A:35 , ASP A:88 , ASP A:90 , ASP A:95 , HOH A:305 , HOH A:312 , HOH A:329BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREILE A:39 , ASP A:41 , ASN A:61 , HOH A:303 , HOH A:317 , HOH A:327BINDING SITE FOR RESIDUE CA A 203
4AC4SOFTWAREASP B:35 , ASP B:41 , ASP B:88 , GLU B:89 , ASP B:90 , HOH B:317BINDING SITE FOR RESIDUE CA B 201
5AC5SOFTWAREILE B:39 , ASP B:41 , ASN B:61 , HOH B:312 , HOH B:319 , HOH B:363BINDING SITE FOR RESIDUE CA B 202
6AC6SOFTWAREASP B:35 , ASP B:88 , ASP B:90 , ASP B:95 , HOH B:305 , HOH B:383 , HOH B:385BINDING SITE FOR RESIDUE CA B 203

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:100 -A:113
2B:100 -B:113

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W57)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W57)

(-) Exons   (0, 0)

(no "Exon" information available for 3W57)

(-) 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:111
 aligned with E2FYL5_SCOMX | E2FYL5 from UniProtKB/TrEMBL  Length:129

    Alignment length:111
                                    28        38        48        58        68        78        88        98       108       118       128 
         E2FYL5_SCOMX    19 EAQLRLYNLRVRGLPSDLMGITDGYVKVFCGSANLGETSVNHNNANPWWTEEFSHFKAQENDILRLEVHDEDTFFDDLLGVCQRQIKVGTHEHDCYLKEGGTLHYMYTLSV 129
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee...........eeeeeee..eeeee...............eeeeee....eeeeeeee......eeeeeeeee...eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3w57 A  19 HMQLRLYNLRVRGLPSDLMGITDGYVKVFCGSANLGETSVNHNNANPWWTEEFSHFKAQENDILRLEVHDEDTFFDDLLGVCQRQIKVGTHEHDCYLKEGGTLHYMYTLSV 129
                                    28        38        48        58        68        78        88        98       108       118       128 


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with E2FYL5_SCOMX | E2FYL5 from UniProtKB/TrEMBL  Length:129

    Alignment length:111
                                    28        38        48        58        68        78        88        98       108       118       128 
         E2FYL5_SCOMX    19 EAQLRLYNLRVRGLPSDLMGITDGYVKVFCGSANLGETSVNHNNANPWWTEEFSHFKAQENDILRLEVHDEDTFFDDLLGVCQRQIKVGTHEHDCYLKEGGTLHYMYTLSV 129
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee...ee..ee..eeeeeee..eeeee...............eeeeee....eeeeeeee......eeeeeeeee...eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3w57 B  19 HMQLRLYNLRVRGLPSDLMGITDGYVKVFCGSANLGETSVNHNNANPWWTEEFSHFKAQENDILRLEVHDEDTFFDDLLGVCQRQIKVGTHEHDCYLKEGGTLHYMYTLSV 129
                                    28        38        48        58        68        78        88        98       108       118       128
   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 3W57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W57)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E2FYL5_SCOMX | E2FYL5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3w57)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3w57
    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
  E2FYL5_SCOMX | E2FYL5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  E2FYL5_SCOMX | E2FYL5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        E2FYL5_SCOMX | E2FYL5: 3w56

(-) Related Entries Specified in the PDB File

3w56