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
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)

(-) Description

Title :  CDIA-CT/CDII TOXIN AND IMMUNITY COMPLEX FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  R. P. Morse, K. Nikolakakis, J. Willet, E. Gerrick, D. A. Low, C. S. Hayes C. W. Goulding
Date :  19 Jul 12  (Deposition) - 12 Dec 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Trnase, Toxin, Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Morse, K. C. Nikolakakis, J. L. Willett, E. Gerrick, D. A. Low, C. S. Hayes, C. W. Goulding
Structural Basis Of Toxicity And Immunity In Contact-Dependent Growth Inhibition (Cdi) Systems.
Proc. Natl. Acad. Sci. Usa V. 109 21480 2012
PubMed-ID: 23236156  |  Reference-DOI: 10.1073/PNAS.1216238110

(-) Compounds

Molecule 1 - ADHESIN/HEMOLYSIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2948-3122
    Gene: BP1026A_3896
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI 1026A
    Organism Taxid: 1085027
    Strain: 1026B
 
Molecule 2 - CDII
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDII
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI 1026A
    Organism Taxid: 1085027
    Strain: 1026B

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1BR8Ligand/IonBROMIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:172 , HOH A:406BINDING SITE FOR RESIDUE BR A 301
2AC2SOFTWAREGLN G:171 , ILE G:172BINDING SITE FOR RESIDUE BR C 302
3AC3SOFTWAREGLN E:171 , ILE E:172BINDING SITE FOR RESIDUE BR E 301
4AC4SOFTWAREASN F:26BINDING SITE FOR RESIDUE BR F 201
5AC5SOFTWAREILE C:172 , HOH C:405BINDING SITE FOR RESIDUE BR G 301
6AC6SOFTWAREASN H:26BINDING SITE FOR RESIDUE BR H 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G6V)

(-) Exons   (0, 0)

(no "Exon" information available for 4G6V)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..........hhhhhhhhhhhhhhhhhhhh...eeee...........eee..eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh.......eeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g6v A 163 GSLSGKPTQIPPLSDEVTTRSLIRENQSAVTLANKGYDVVQNPEVLGPKNPDYTINGQVFDNYAPATGNVRNIATTISNKVSSGQASNIVVNLADSSASPAAIEAQINSYPIPGLGKVIVIDKLGNITIIKP 294
                                   172       182       192       202       212       222       232       242       252       262       272       282       292  


Chain B from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhh..eee...ee.hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhh.....eeeee...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4g6v B   2 AIDLFCYLSIDRGAAESDLNKIRSNHSELFEGKFLISPVRDADFSLKEIAAEHGLVAESFFLVSLNDKNSADLIPIVSKILVDGFNGGAILILQDNEYRRTSL 104
                                    11        21        31        41        51        61        71        81        91       101   


Chain C from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..........hhhhhhhhhhhhhhhhhhhh...eeee...........eee..eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh.......eeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g6v C 163 GSLSGKPTQIPPLSDEVTTRSLIRENQSAVTLANKGYDVVQNPEVLGPKNPDYTINGQVFDNYAPATGNVRNIATTISNKVSSGQASNIVVNLADSSASPAAIEAQINSYPIPGLGKVIVIDKLGNITIIKP 294
                                   172       182       192       202       212       222       232       242       252       262       272       282       292  


Chain D from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhh..eee...ee.hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhh.....eeeee...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4g6v D   2 AIDLFCYLSIDRGAAESDLNKIRSNHSELFEGKFLISPVRDADFSLKEIAAEHGLVAESFFLVSLNDKNSADLIPIVSKILVDGFNGGAILILQDNEYRRTSL 104
                                    11        21        31        41        51        61        71        81        91       101   


Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..........hhhhhhhhhhhhhhhhhhhhh..eeee...........eee..eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh.......eeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g6v E 163 GSLSGKPTQIPPLSDEVTTRSLIRENQSAVTLANKGYDVVQNPEVLGPKNPDYTINGQVFDNYAPATGNVRNIATTISNKVSSGQASNIVVNLADSSASPAAIEAQINSYPIPGLGKVIVIDKLGNITIIKP 294
                                   172       182       192       202       212       222       232       242       252       262       272       282       292  


Chain F from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhh..eee...ee.hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4g6v F   2 AIDLFCYLSIDRGAAESDLNKIRSNHSELFEGKFLISPVRDADFSLKEIAAEHGLVAESFFLVSLNDKNSADLIPIVSKILVDGFNGGAILILQDNEYRRT 102
                                    11        21        31        41        51        61        71        81        91       101 


Chain G from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..........hhhhhhhhhhhhhhhhhhhhh..eeee...........eee..eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh.......eeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g6v G 163 GSLSGKPTQIPPLSDEVTTRSLIRENQSAVTLANKGYDVVQNPEVLGPKNPDYTINGQVFDNYAPATGNVRNIATTISNKVSSGQASNIVVNLADSSASPAAIEAQINSYPIPGLGKVIVIDKLGNITIIKP 294
                                   172       182       192       202       212       222       232       242       252       262       272       282       292  


Chain H from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhhh..eee...ee.hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4g6v H   2 AIDLFCYLSIDRGAAESDLNKIRSNHSELFEGKFLISPVRDADFSLKEIAAEHGLVAESFFLVSLNDKNSADLIPIVSKILVDGFNGGAILILQDNEYRRT 102
                                    11        21        31        41        51        61        71        81        91       101
   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 4G6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G6V)

(-) Gene Ontology  (13, 13)

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
    BR  [ 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 4g6v)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 ](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
  4g6v
    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
  CDIA2_BURP2 | I1WVY3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CDII2_BURP2 | P0DMJ7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  H9T8H3_BURPE | H9T8H3
    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
  CDIA2_BURP2 | I1WVY3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CDII2_BURP2 | P0DMJ7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  H9T8H3_BURPE | H9T8H3
    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 4G6V)

(-) Related Entries Specified in the PDB File

4g6u