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 :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF WZT
 
Authors :  M. S. Kimber, L. Cuthbertson, C. Whitfield
Date :  04 Sep 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Abc Transporter, Immunoglobulin Fold, Carbohydrate Binding, Domain Swapping, O Antigen Export, Atp-Binding, Nucleotide- Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cuthbertson, M. S. Kimber, C. Whitfield
Substrate Binding By A Bacterial Abc Transporter Involved In Polysaccharide Export.
Proc. Natl. Acad. Sci. Usa V. 104 19529 2007
PubMed-ID: 18032609  |  Reference-DOI: 10.1073/PNAS.0705709104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE ATP BINDING COMPONENT OF ABC- TRANSPORTER
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: ORF431
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: O9A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2NA5Ligand/IonSODIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:402 , HOH A:463BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWAREARG A:356 , SER B:300 , ALA B:301 , GLY B:302 , HOH B:505BINDING SITE FOR RESIDUE CL A 2
3AC3SOFTWAREARG A:356 , HOH A:544 , SER B:426 , PHE B:427BINDING SITE FOR RESIDUE CL A 8
4AC4SOFTWARELEU B:335 , LYS B:337 , LEU B:383 , LEU B:384 , SER B:385 , ASP B:405BINDING SITE FOR RESIDUE NA B 9
5AC5SOFTWAREGLY A:289 , LEU A:400 , TYR B:284 , HOH B:446BINDING SITE FOR RESIDUE NA B 10
6AC6SOFTWARETYR A:284 , GLY B:289 , LEU B:400 , HOH B:436BINDING SITE FOR RESIDUE NA A 11
7AC7SOFTWAREASP A:422 , HOH A:551 , HOH A:585 , TYR B:345 , HOH B:599BINDING SITE FOR RESIDUE NA B 12
8AC8SOFTWARETYR A:345 , HOH A:434 , ASP B:422 , LYS B:424 , HOH B:447BINDING SITE FOR RESIDUE NA A 13
9AC9SOFTWARETYR A:284 , TRP A:286 , HOH A:587 , GLN B:288 , ASN B:392 , GLN B:394BINDING SITE FOR RESIDUE PG4 A 432

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R5O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R5O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R5O)

(-) Exons   (0, 0)

(no "Exon" information available for 2R5O)

(-) 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:167
 aligned with Q47591_ECOLX | Q47591 from UniProtKB/TrEMBL  Length:431

    Alignment length:167
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       
         Q47591_ECOLX   264 MSLDEIEDVYHTRPGYRPEEYRWGQGGAKIIDYHIQSAGVDFPPSLTGNQQTDFLMKVVFEYDFDCVVPGILIKTLDGLFLYGTNSFLASEGRENISVSRGDVRVFKFSLPVDLNSGDYLLSFGISAGNPQTDMTPLDRRYDSIILHVTKSMDFWGVIDLKSSFTSY 430
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------2r5oA01 A:272-422 abc- transporter (atp binding component) like domain                                                                                 -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.......eee....eeeeeeeeee..ee....ee...eeeeeeeeee...eeeeeeeeeeee....eeeeeehhhhh.....eee....eeeeeeeee.....eeeeeeeeeeeee...eeeeeeeeeeeeeeeee.....ee......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5o A 264 MSLDEIEDVYHTRPGYRPEEYRWGQGGAKIIDYHIQSAGVDFPPSLTGNQQTDFLMKVVFEYDFDCVVPGILIKTLDGLFLYGTNSFLASEGRENISVSRGDVRVFKFSLPVDLNSGDYLLSFGISAGNPQTDMTPLDRRYDSIILHVTKSMDFWGVIDLKSSFTSY 430
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q47591_ECOLX | Q47591 from UniProtKB/TrEMBL  Length:431

    Alignment length:166
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423      
         Q47591_ECOLX   264 MSLDEIEDVYHTRPGYRPEEYRWGQGGAKIIDYHIQSAGVDFPPSLTGNQQTDFLMKVVFEYDFDCVVPGILIKTLDGLFLYGTNSFLASEGRENISVSRGDVRVFKFSLPVDLNSGDYLLSFGISAGNPQTDMTPLDRRYDSIILHVTKSMDFWGVIDLKSSFTS 429
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------2r5oB01 B:272-422 abc- transporter (atp binding component) like domain                                                                                 ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.......eee....eeeeeeeeee..ee.........eeeeeeeeee...eeeeeeeeeeee....eeeeeehhhhh.....eee....eeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeeee..............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5o B 264 MSLDEIEDVYHTRPGYRPEEYRWGQGGAKIIDYHIQSAGVDFPPSLTGNQQTDFLMKVVFEYDFDCVVPGILIKTLDGLFLYGTNSFLASEGRENISVSRGDVRVFKFSLPVDLNSGDYLLSFGISAGNPQTDMTPLDRRYDSIILHVTKSMDFWGVIDLKSSFTS 429
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423
   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 2R5O)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R5O)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q47591_ECOLX | Q47591)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r5o)
 
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
  2r5o
    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
  Q47591_ECOLX | Q47591
    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
  Q47591_ECOLX | Q47591
    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 2R5O)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2R5O)