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 :  PSEUDOMANAS EXOTOXIN A IN COMPLEX WITH THE PJ34 INHIBITOR
 
Authors :  S. P. Yates, P. J. Taylor, R. Joergensen, D. Ferrraris, J. Zhang, G. R. Andersen, A. R. Merrill
Date :  28 Sep 04  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Toxin, Adp-Ribosylation, Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Yates, P. J. Taylor, R. Joergensen, D. Ferrraris, J. Zhang, G. R. Andersen, A. R. Merrill
Structure-Function Analysis Of Water-Soluble Inhibitors Of The Catalytic Domain Of Exotoxin A From Pseudomonas Aeruginosa
Biochem. J. V. 385 667 2005
PubMed-ID: 15458385  |  Reference-DOI: 10.1042/BJ20041480
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXOTOXIN A
    Chains: A, B
    EC Number: 2.4.2.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PE(DELTA)5-399
    Expression System Strain: BB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC FRAGMENT, PE24H
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: NAD-DEPENDENT ADP-RIBOSYLTRANSFERASE

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1P342Ligand/IonN~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1P341Ligand/IonN~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1P341Ligand/IonN~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:440 , GLY A:441 , TYR A:470 , ILE A:471 , ALA A:478 , TYR A:481 , GLN A:485 , HOH A:1051BINDING SITE FOR RESIDUE P34 A 1001
2AC2SOFTWAREHIS B:440 , GLY B:441 , TYR B:470 , ILE B:471 , TYR B:481 , GLN B:485 , GLU B:553 , HOH B:2098BINDING SITE FOR RESIDUE P34 B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XK9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:535 -Pro A:536
2Leu B:535 -Pro B:536

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XK9)

(-) Exons   (0, 0)

(no "Exon" information available for 1XK9)

(-) 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:204
 aligned with TOXA_PSEAE | P11439 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:204
                                   433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623    
           TOXA_PSEAE   424 EFLGDGGDISFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARSQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTGLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYAS 627
               SCOP domains d1xk9a_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 1xk9A00 A:399-602 Diphtheria Toxin, domain 1                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhh...............eeee.hhhhhhh................eeeeeeee.hhhh.eee........hhhhhhhhhhh........eeeee......eeeeehhhhhh..eeee..............hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xk9 A 399 EFLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARSQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYAS 602
                                   408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598    


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with TOXA_PSEAE | P11439 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:204
                                   433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623    
           TOXA_PSEAE   424 EFLGDGGDISFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARSQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTGLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYAS 627
               SCOP domains d1xk9b_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 1xk9B00 B:399-602 Diphtheria Toxin, domain 1                                                                                                                                                                 CATH domains
           Pfam domains (1) Exotox-A_cataly-1xk9B01 B:399-602                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) Exotox-A_cataly-1xk9B02 B:399-602                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhhh....------....eee..hhhhhhh................eeeeeeee.hhhh.eee.........hhhhhhhhhh........eeeee......eeeeehhhhhh..eeee..............hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xk9 B 399 EFLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRAR------IWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYAS 602
                                   408       418       428       438       448       458      |468       478       488       498       508       518       528       538       548       558       568       578       588       598    
                                                                                     458    465
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Exotox-A_cataly] (4)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TOXA_PSEAE | P11439)
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 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
    P34  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:535 - Pro A:536   [ RasMol ]  
    Leu B:535 - Pro B:536   [ RasMol ]  
 
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
  1xk9
    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
  TOXA_PSEAE | P11439
    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
  TOXA_PSEAE | P11439
    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
        TOXA_PSEAE | P11439: 1aer 1dma 1ikp 1ikq 1zm2 1zm3 1zm4 1zm9 2zit 3b78 3b82 3b8h

(-) Related Entries Specified in the PDB File

1aer STRUCTURE OF EXOTOXIN A IN COMPLEX WITH NAD ANALOGUE