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 :  CRYSTAL STRUCTURE OF PUTATIVE PORE-FORMING TOXIN (YP_001301288.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Nov 09  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Pore-Forming Toxin, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Pore-Forming Toxin (Yp_001301288. 1) From Bacteroides Vulgatus Atcc 8482 At 1. 8 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PORE-FORMING TOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BVU_4064
    Organism Scientific: BACTEROIDES VULGATUS ATCC 8482
    Organism Taxid: 435590
    Strain: ATCC 8482 / DSM 1447 / NCTC 11154

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:390 , HOH A:391BINDING SITE FOR RESIDUE ACT A 1
2AC2SOFTWARESER A:130BINDING SITE FOR RESIDUE ACT A 2
3AC3SOFTWAREHOH A:13 , GLU A:115 , VAL A:116 , THR A:117 , SER A:164 , TYR A:185 , HOH A:311 , HOH A:410BINDING SITE FOR RESIDUE GOL A 4
4AC4SOFTWAREHOH A:25 , ASP A:59 , VAL A:60 , THR A:61 , GLN A:62 , HOH A:319 , HOH A:328BINDING SITE FOR RESIDUE GOL A 5
5AC5SOFTWAREGLN A:110 , ASP A:212 , HOH A:305BINDING SITE FOR RESIDUE MRD A 6
6AC6SOFTWARESER A:83 , SER A:85 , THR A:102BINDING SITE FOR RESIDUE MRD A 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KOG)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KOG)

(-) 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:226
 aligned with A6L7K2_BACV8 | A6L7K2 from UniProtKB/TrEMBL  Length:282

    Alignment length:228
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258        
         A6L7K2_BACV8    39 TPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGMTGSASVTIPALKAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYNKGVREDKVTLNDVQVLAHSRFSVFVDYMKTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGH 266
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeee......hhhhheeee.....eee.......eeeeeeeee..eeeeeeeee.......eeeeeeeeee...eeeeeeeeeeeeeeeee...eee.....eeeeeeeeeeeeeeeeee.....hhhhhhhhhhh..eeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeee...--...eeeeeeeeeeeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kog A  39 TPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGmTGSASVTIPALKAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYNKGVREDKVTLNDVQVLAHSRFSVFVDYmKTTSVYQIIEKSP--DGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGH 266
                                    48        58        68        78        88      | 98       108       118       128       138       148       158       168       178       188       198       208     | 218        |- |     238       248       258        
                                                                                   95-MSE                                                                                                                214-MSE      227  |                                    
                                                                                                                                                                                                                         230
   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 3KOG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KOG)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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
    Thr A:78 - Pro A:79   [ RasMol ]  
 

(-) 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
  3kog
    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
  A6L7K2_BACV8 | A6L7K2
    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
  A6L7K2_BACV8 | A6L7K2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KOG)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KOG)