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 :  CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-I
 
Authors :  R. Jorgensen, P. R. Edwards, A. R. Merrill
Date :  31 Oct 09  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Adp-Ribosyl Transferase, Alpha-Beta Complex, Diphthamide, Transferase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Jorgensen, P. R. Edwards, A. R. Merrill
Structure Function Analysis Of Soluble Inhibitors Of Cholix Toxin From Vibrio Cholerae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHOLIX TOXIN
    Chains: A
    EC Number: 2.4.2.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28+
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 459-665
    Gene: CHXA, TOXA
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: TP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1G9I1Ligand/Ion2-{2-[4-(PYRROLIDIN-1-YLMETHYL)PHENYL]ETHYL}-5,6-DIHYDROIMIDAZO[4,5,1-JK][1,4]BENZODIAZEPIN-7(4H)-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:107 , HOH A:152 , HIS A:460 , GLY A:461 , TRP A:489 , TYR A:493 , VAL A:494 , ALA A:501 , TYR A:504 , GLU A:581BINDING SITE FOR RESIDUE G9I A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KI7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:563 -Pro A:564

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KI7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KI7)

(-) Exons   (0, 0)

(no "Exon" information available for 3KI7)

(-) 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:199
 aligned with CHXA_VIBCL | Q5EK40 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:208
                                   467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657        
           CHXA_VIBCL   458 RAVITPQGVTNWTYQELEATHQALTREGYVFVGYHGTNHVAAQTIVNRIAPVPRGNNTENEEKWGGLYVATHAEVAHGYARIKEGTGEYGLPTRAERDARGVMLRVYIPRASLERFYRTNTPLENAEEHITQVIGHSLPLRNEAFTGPESAGGEDETVIGWDMAIHAVAIPSTIPGNAYEELAIDEEAVAKEQSISTKPPYKERKDEL 665
               SCOP domains d3ki7a_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..hhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhh....---------.....eee..hhhhhhh........hhhhh.hhhhhhh..eeeeeeee.hhhh.eee...hhhhhhhhhhhhhh........eeeee......eeeeehhhhhh..eeeeeeee.........hhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ki7 A 426 MAVITPQGVTNWTYQELEATHQALTREGYVFVGYHGTNHVAAQTIVNRIAPV---------EKWGGLYVATHAEVAHGYARIKEGTGEYGLPTRAERDARGVMLRVYIPRASLERFYRTNTPLENAEEHITQVIGHSLPLRNEAFTGPESAGGEDETVIGWDMAIHAVAIPSTIPGNAYEELAIDEEAVAKEQSISTKPPYKERKDEL 633
                                   435       445       455       465       475 |       - |     495       505       515       525       535       545       555       565       575       585       595       605       615       625        
                                                                             477       487
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KI7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KI7)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHXA_VIBCL | Q5EK40)
molecular function
    GO:0047286    NAD+-diphthamide ADP-ribosyltransferase activity    Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).

 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
    G9I  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:563 - Pro A:564   [ 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
  3ki7
    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
  CHXA_VIBCL | Q5EK40
    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)
  2.4.2.36
    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
  CHXA_VIBCL | Q5EK40
    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
        CHXA_VIBCL | Q5EK40: 2q5t 2q6m 3ess 3ki0 3ki1 3ki2 3ki3 3ki4 3ki5 3ki6 3ny6 3q9o

(-) Related Entries Specified in the PDB File

2q5t FULL-LENGTH CHOLIX TOXIN FROM VIBRIO CHOLERAE
2q6m CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH THE PJ34 INHIBITOR
3ess CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH THE 1,8-NAPHTHALIMIDE INHIBITOR
3ki0 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-D
3ki1 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-F
3ki2 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-G
3ki3 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-H
3ki4 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-P
3ki5 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-M
3ki6 CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH INHIBITOR GP-L