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 :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA DSBA E82I IN COMPLEX WITH MIPS-0000851 (3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE)
 
Authors :  R. M. Mcmahon, J. L. Martin
Date :  24 Aug 15  (Deposition) - 05 Oct 16  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mohanty, K. Rimmer, R. M. Mcmahon, S. J. Headey, M. Vazirani, S. R. Shouldice, M. Coincon, S. Tay, C. J. Morton, J. S. Simpson, J. L. Martin, M. J. Scanlon
Fragment Library Screening Identifies Hits That Bind To The Non-Catalytic Surface Of Pseudomonas Aeruginosa Dsba1.
Plos One V. 12 73436 2017
PubMed-ID: 28346540  |  Reference-DOI: 10.1371/JOURNAL.PONE.0173436

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DSBA, PA5489
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
11YO1Ligand/Ion3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE
2GOL4Ligand/IonGLYCEROL
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:20 , SER A:22 , GLU A:28 , LEU A:79 , GLN A:137 , LYS A:140 , LEU A:144 , TYR A:148 , HOH A:355 , HOH A:382binding site for residue 1YO A 201
2AC2SOFTWARECYS A:37 , GLY A:152 , VAL A:153 , ARG A:187 , GOL A:205 , HOH A:333 , HOH A:340 , HOH A:409binding site for residue GOL A 202
3AC3SOFTWARELYS A:10 , VAL A:13 , GLY A:117 , ARG A:163 , PHE A:164 , ASP A:165 , HOH A:307 , HOH A:329binding site for residue GOL A 203
4AC4SOFTWAREALA A:147binding site for residue GOL A 204
5AC5SOFTWAREGLY A:25 , ILE A:27 , ASP A:57 , TRP A:71 , LYS A:191 , GOL A:202 , HOH A:309binding site for residue GOL A 205
6AC6SOFTWAREHIS A:39 , THR A:151 , GLY A:152 , ASP A:165 , GLY A:167 , HOH A:339binding site for residue MES A 206

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:40

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:153 -Pro A:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCH)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee............eeeeeee...hhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dch A   5 DYTAGKEYVELSSPVPVSQPGKIEVVELFWYGCPHCYAFEPTIVPWSEKLPADVHFVRLPALFGGIWNVHGQMFLTLISMGVEHDVHNAVFEAIHKEHKKLATPEEMADFLAGKGVDKEKFLSTYNSFAIKGQMEKAKKLAMAYQVTGVPTMVVNGKYRFDIGSAGGPEETLKLADYLIEKERAAAK 191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
   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 5DCH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    1YO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ 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
    Val A:153 - Pro A:154   [ 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
  5dch
    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
  DSBA_PSEAE | P0C2B2
    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)
  (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
  DSBA_PSEAE | P0C2B2
    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
        DSBA_PSEAE | P0C2B2: 2mbt 3h93 4zl7 4zl8 4zl9 5tlq

(-) Related Entries Specified in the PDB File

2mbu 2MBU CONTAINS THE SAME PROTEIN-LIGAND COMPLEX DETERMINED BY SOLUTION NMR METHODS.
4zl7
4zl8
4zl9