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 :  SQUARE-SHAPED OCTAMERIC STRUCTURE OF KTRA WITH ATP BOUND
 
Authors :  R. S. Vieira-Pires, J. H. Morais-Cabral
Date :  15 Feb 13  (Deposition) - 17 Apr 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.24
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Square-Shaped Octameric Ring, Rck Domain, Potassium Transport Regulation, Ktrb Membrane Protein, Cytosol, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Vieira-Pires, A. Szollosi, J. H. Morais-Cabral
The Structure Of The Ktrab Potassium Transporter
Nature V. 496 323 2013
PubMed-ID: 23598340  |  Reference-DOI: 10.1038/NATURE12055

(-) Compounds

Molecule 1 - KTR SYSTEM POTASSIUM UPTAKE PROTEIN A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Gene: KTRA, YUAA, BSU31090
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: K(+)-UPTAKE PROTEIN KTRA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1ATP8Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , GLY A:15 , ARG A:16 , PHE A:17 , ASP A:36 , ILE A:37 , LYS A:41 , ALA A:55 , ASN A:56 , ALA A:57 , ALA A:77 , ILE A:78 , GLY A:79 , ALA A:80 , LYS A:103 , GLU A:125 , ARG B:16 , GLU B:125BINDING SITE FOR RESIDUE ATP A 601
2AC2SOFTWAREARG A:16 , GLY B:13 , LEU B:14 , GLY B:15 , ARG B:16 , PHE B:17 , ASP B:36 , ILE B:37 , LYS B:41 , ALA B:55 , ASN B:56 , ALA B:57 , ALA B:77 , ILE B:78 , GLY B:79 , ALA B:80 , LYS B:103 , GLU B:125BINDING SITE FOR RESIDUE ATP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J90)

(-) Exons   (0, 0)

(no "Exon" information available for 4J90)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.eeee....hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhhhhhhhhhhhhh..eeeeee....eeeeeee.hhhhh.ee....hhhhhh..eeeeeee..eeee......ee....eeeeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j90 A   6 NKQFAVIGLGRFGGSICKELHRMGHEVLAVDINEEKVNAYASYATHAVIANATEENELLSLGIRNFEYVIVAIGANIQASTLTTLLLKELDIPNIWVKAQNYYHHKVLEKIGADRIIHPEKDMGVKIAQSLSDENVLNYIDLSDEYSIVELLATRKLDSKSIIDLNVRAKYGCTILAIKHHGDICLSPAPEDIIREQDCLVIMGHKKDIKRFENEGM 222
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.eeee....hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhhhhhhhhhhhhh..eeeeee....eeeeeee.......ee............eeeeeee..eeee......ee....eeeeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j90 B   6 NKQFAVIGLGRFGGSICKELHRMGHEVLAVDINEEKVNAYASYATHAVIANATEENELLSLGIRNFEYVIVAIGANIQASTLTTLLLKELDIPNIWVKAQNYYHHKVLEKIGADRIIHPEKDMGVKIAQSLSDENVLNYIDLSDEYSIVELLATRKLDSKSIIDLNVRAKYGCTILAIKHHGDICLSPAPEDIIREQDCLVIMGHKKDIKRFENEGM 222
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
   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 4J90)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J90)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J90)

(-) Gene Ontology  (7, 7)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4j90)
 
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
  4j90
    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
  KTRA_BACSU | O32080
    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
  KTRA_BACSU | O32080
    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
        KTRA_BACSU | O32080: 1lsu 2hms 2hmt 2hmu 2hmv 2hmw 4j7c 4j91 5but

(-) Related Entries Specified in the PDB File

2hms RECTANGULAR-SHAPED OCTAMERIC RING STRUCTURE OF AN RCK DOMAIN WITH NADH BOUND
2hmt DIAMOND-SHAPED OCTAMERIC RING STRUCTURE OF AN RCK DOMAIN WITH NADH BOUND
2hmu DIAMOND-SHAPED OCTAMERIC RING STRUCTURE OF AN RCK DOMAIN WITH ATP BOUND
2hmv DIAMOND-SHAPED OCTAMERIC RING STRUCTURE OF AN RCK DOMAIN WITH ADP BOUND
2hmw SQUARE-SHAPED OCTAMERIC RING STRUCTURE OF AN RCK DOMAIN WITH ATP BOUND
4j91