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 AND FUNCTIONAL CHARACTERIZATION OF PSEUDOMONAS AERUGINOSA ALGX
 
Authors :  L. M. Riley, J. T. Weadge, P. Baker, H. Robinson, J. D. C. Codee, P. A. Tipt D. E. Ohman, P. L. Howell
Date :  09 May 13  (Deposition) - 26 Jun 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Alginate Acetylation, Sgnh Hydrolase, Carbohydrate-Binding Domain, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Riley, J. T. Weadge, P. Baker, H. Robinson, J. D. Codee, P. A. Tipton, D. E. Ohman, P. L. Howell
Structural And Functional Characterization Of Pseudomonas Aeruginosa Algx: Role Of Algx In Alginate Acetylation.
J. Biol. Chem. V. 288 22299 2013
PubMed-ID: 23779107  |  Reference-DOI: 10.1074/JBC.M113.484931

(-) Compounds

Molecule 1 - ALGINATE BIOSYNTHESIS PROTEIN ALGX
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24B
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-474
    Gene: ALGX, PA3546
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4KNC)

(-) Sites  (0, 0)

(no "Site" information available for 4KNC)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:44 -A:229
2A:347 -A:460
3B:44 -B:229
4B:347 -B:460

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr B:62 -His B:63
2Thr A:62 -His A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KNC)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhh...eee.....eeehhhhh......hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh................hhhhhhhhhhhhhhhhh...hhhhh....eeeeeeeeeee.hhhhhhhhhhhh.....eeeeeeeeee.....eeee.hhhhh...hhhhhhhhhhh..eee........hhhhhhhh.hhhhhhh...eeeeeee......hhhhhhhhhhhhh.......eeeeeeee......eeee.......hhh.eeeeeee......eeeeeeee....eeeeeee.........eeeee...........eeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knc A  41 GNLCPAAAYDSRYNTKYLGFFTHLVQAQDDWLFRTTYDLRTDFGTSAEGWRELRALRDELKRKGIELVVVYQPTRGLVNREKLSPAEKAGFDYELAKKNYLATIARFRQAGIWTPDFSPLFDEKEEHAYYFKGDHHWTPHGARRSAKIVAETLKQVPGFEEIPKKQFESKRVGLLSKLGTFHKAAAQLCGNSYATQYVDRFETEPVGNPQIALVGTSNSGPAYNFAGFLEEFSGADILNNAVSGGGFDSSLLAYMTSEEFHKNPPKILIWEFATHYDMAQKSFYRQAMPLVDNGCSGRKTVLSRKVKLRQGRNEVLLNSAALPIRSGSYVADVTYSDPSVHELKNTIWYMNGRREQLKIEQSKAVDTGGRYVFQLRNDSDWADQQFLSLEIEAPDMPQGLEVQASICQAA 463
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     ||262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442   ||  453       463
                                                                                                                                                                                                                                       246|                                                                                                                                                                                        446|               
                                                                                                                                                                                                                                        259                                                                                                                                                                                         448               


Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhh..eee.....eee...........hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh................hhhhhhhhhhhhhhhhhhh.hhhhh...eeeeeeeeeeee.hhhhhhhhhhhh.....eeeeeeeeeee...hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh........eeeeeeee....eeeeee.......hhh.eeeeeee......eeeeeeee....eeeeeee.........eeeee...........eeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knc B  42 NLCPAAAYDSRYNTKYLGFFTHLVQAQDDWLFRTTYDLRTDFGTSAEGWRELRALRDELKRKGIELVVVYQPTRGLVNREKLSPAEKAGFDYELAKKNYLATIARFRQAGIWTPDFSPLFDEKEEHAYYFKGDHHWTPHGARRSAKIVAETLKQVPGFEEIPKKQFESKRVGLLSKLGTFHKAAAQLCGNSYATQYVDRFETEPVGASGDLFGDGGNPQIALVGTSNSGPAYNFAGFLEEFSGADILNNAVSGGGFDSSLLAYMTSEEFHKNPPKILIWEFATHYDMAQKSFYRQAMPLVDNGCSGRKTVLSRKVKLRQGRNEVLLNSAALPIRSGSYVADVTYSDPSVHELKNTIWYMNGRREQLKIEQSKAVDTGGRYVFQLRNDSDWADQQFLSLEIEAPDMPQGLEVQASICQAA 463
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443  ||   454         
                                                                                                                                                                                                                                         249|                                                                                                                                                                                               446|               
                                                                                                                                                                                                                                          252                                                                                                                                                                                                448
   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 4KNC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 4knc)
 
  Sites
(no "Sites" information available for 4knc)
 
  Cis Peptide Bonds
    Thr A:62 - His A:63   [ RasMol ]  
    Thr B:62 - His B:63   [ 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 | 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
  4knc
    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
  ALGX_PSEAE | Q51372
    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
  ALGX_PSEAE | Q51372
    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 4KNC)

(-) Related Entries Specified in the PDB File

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