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
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)

(-) Description

Title :  NEW TYPE VI-SECRETED TOXINS AND SELF-RESISTANCE PROTEINS IN SERRATIA MARCESCENS
 
Authors :  G. English, K. Trunk, V. A. Rao, V. Srikannathasan, M. J. Fritsch, M. Guo W. N. Hunter, S. J. Coulthurst
Date :  07 Jun 12  (Deposition) - 19 Sep 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Toxin, Resistance Protein, Helical Fold, S-Sad Phasing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. English, K. Trunk, V. A. Rao, V. Srikannathasan, W. N. Hunter, S. J. Coulthurst
New Secreted Toxins And Immunity Proteins Encoded Within The Type Vi Secretion System Gene Cluster Of Serratia Marcescens
Mol. Microbiol. V. 86 921 2012
PubMed-ID: 22957938  |  Reference-DOI: 10.1111/MMI.12028

(-) Compounds

Molecule 1 - RAP1B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BTEV_PSC503
    Expression System Strain: ROSETTA-GAMI (DE3)
    Expression System Taxid: 562
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Strain: DB10

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2IOD2Ligand/IonIODIDE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2IOD4Ligand/IonIODIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:106 , HOH A:2008BINDING SITE FOR RESIDUE IOD A1151
2AC2SOFTWAREARG A:53 , ARG A:77 , PHE A:82 , ILE A:84 , ASP A:88 , HOH A:2028BINDING SITE FOR RESIDUE IOD A1152
3AC3SOFTWAREASN A:140 , ARG A:143BINDING SITE FOR RESIDUE EDO A1153
4AC4SOFTWAREARG A:134 , ASP A:142 , HOH A:2021BINDING SITE FOR RESIDUE EDO A1154
5AC5SOFTWARELYS A:47 , HIS A:125 , HOH A:2024 , HOH A:2080BINDING SITE FOR RESIDUE EDO A1155
6AC6SOFTWARETYR A:98 , GLU A:128 , HOH A:2079 , HOH A:2087 , HOH A:2111BINDING SITE FOR RESIDUE EDO A1156
7AC7SOFTWAREARG A:71 , HOH A:2109BINDING SITE FOR RESIDUE EDO A1157

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:54 -A:120

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AX2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AX2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AX2)

(-) Exons   (0, 0)

(no "Exon" information available for 4AX2)

(-) 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:124
 aligned with K4DIE5_SERMA | K4DIE5 from UniProtKB/TrEMBL  Length:125

    Alignment length:128
                               1                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117        
         K4DIE5_SERMA     - ---MAPIQDPVAFIKQMPYHQVVKELALSRCLAQVSDSDKAFSLDAARTANAMREWMPFDIESGDEKINVLIDKYKSRINEFHSETKDKSQGVTLNCLRLYHSPELDKLSRQLIAGNPDRTWNQDNAK 125
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........----...hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ax2 A  24 QGHMAPIQDPVAFIKQMPYHQVVKELALSRCLAQVSDSDKAFSLDAARTANAMREWMPFDIESGDEKINVLIDKYKSRINEFHS----KSQGVTLNCLRLYHSPELDKLSRQLIAGNPDRTWNQDNAK 151
                                    33        43        53        63        73        83        93       103   |   113       123       133       143        
                                                                                                             107  112
   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 4AX2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AX2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AX2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4AX2)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ax2)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4ax2
    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
  K4DIE5_SERMA | K4DIE5
    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
  K4DIE5_SERMA | K4DIE5
    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 4AX2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4AX2)