Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL ANALYSIS AND INHIBITION OF TRAE FROM THE PKM101 TYPE IV SECRETION SYSTEM
 
Authors :  B. Casu, J. Sygusch, C. Baron
Date :  19 Feb 16  (Deposition) - 28 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Bacterial Secretion, Type Iv Secretion, Virb, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Casu, J. Smart, M. A. Hancock, M. Smith, J. Sygusch, C. Baron
Structural Analysis And Inhibition Of Trae From The Pkm101 Type Iv Secretion System.
J. Biol. Chem. V. 291 23817 2016
PubMed-ID: 27634044  |  Reference-DOI: 10.1074/JBC.M116.753327

(-) Compounds

Molecule 1 - CONJUGAL TRANSFER PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 469008
    Expression System Vector: PHT
    Fragment: RESIDUES 42-204
    Gene: TRAE, B634_00049, ECONIH1_27615, PEC386IL_00125, PECNDM0_00049, PHKU1_33, PKC394-028, PKC396-021, PMUR050_041, PN3_023, PU53_15805
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CONJUGAL TRANSFER PROTEIN TRAE,TRAE,TRAE PROTEIN,INNER MEMBRANE PROTEIN FORMS CHANNEL FOR TYPE IV SECRETION OF T-DNA COMPLEX,VIRB8,TYPE IV SECRETION OF T-DNA VIRB8,UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5I97)

(-) Sites  (0, 0)

(no "Site" information available for 5I97)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I97)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I97)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I97)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I97)

(-) Exons   (0, 0)

(no "Exon" information available for 5I97)

(-) 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeeeehhh.eeeeeeeeeeee.........eeeeeeeeeee.....hhhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i97 A  88 TRDQTSYGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKGRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPE 230
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227   


Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeeeehhh.eeeeeeeeeeee.........eeeeeeeeeee.....hhhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i97 B  89 RDQTSYGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKGRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPE 230
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228  


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeeeehhh.eeeeeeeeeeee.........eeeeeeeeeee.......hhhhh....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i97 C  94 YGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKGRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPE 230
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeeeehhh.eeeeeeeeeeee.........eeeeeeeeeee................eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i97 D  94 YGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKGRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPE 230
                                   103       113       123       133       143       153       163       173       183       193       203       213       223
   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 5I97)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I97)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I97)

(-) Gene Ontology  (3, 3)

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
(no "Ligands, Modified Residues, Ions" information available for 5i97)
 
  Sites
(no "Sites" information available for 5i97)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5i97)
 
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 | Biol. Unit 1 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
  5i97
    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
  Q17U16_ECOLX | Q17U16
    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
  Q17U16_ECOLX | Q17U16
    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 5I97)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I97)