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 :  INTERMEDIATE GATING STRUCTURE 2 OF THE INWARDLY RECTIFYING K+ CHANNEL KIRBAC3.1
 
Authors :  J. M. Gulbis, A. Kuo, B. Smith, D. A. Doyle, A. Edwards, C. Arrowsmith, M.
Date :  30 Sep 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Integral Membrane Protein, Ion Channel, Inwardly Rectifying K+ Channel, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Gulbis, A. Kuo, B. Smith, D. A. Doyle, A. Edwards, C. Arrowsmith, M. Sundstrom
Two Intermediate Gating State Crystal Structures Of The Kirbac3. 1 K+ Channel
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INWARD RECTIFIER POTASSIUM CHANNEL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30A
    Expression System Strain: BL-21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MAGNETOSPIRILLUM MAGNETOTACTICUM
    Organism Taxid: 188

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1K7Ligand/IonPOTASSIUM ION
2MG1Ligand/IonMAGNESIUM ION
3SPM1Ligand/IonSPERMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3SPM2Ligand/IonSPERMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:98 , TYR A:99 , K A:1004 , GLY B:98 , TYR B:99BINDING SITE FOR RESIDUE K A 1002
2AC2SOFTWARETHR A:96 , K A:1006 , THR B:96 , K B:1005BINDING SITE FOR RESIDUE K A 1003
3AC3SOFTWAREILE A:97 , GLY A:98 , K A:1002 , HOH A:2002 , ILE B:97 , GLY B:98 , K B:1005 , HOH B:3002BINDING SITE FOR RESIDUE K A 1004
4AC4SOFTWARETHR A:96 , ILE A:97 , K A:1003 , HOH A:2003 , THR B:96 , ILE B:97 , HOH B:3002BINDING SITE FOR RESIDUE K A 1006
5AC5SOFTWARETHR A:96 , HOH A:2003 , THR B:96BINDING SITE FOR RESIDUE MG A 2001
6AC6SOFTWARETHR A:96 , ILE A:97 , K A:1003 , K A:1004 , HOH A:2003 , THR B:96 , ILE B:97 , HOH B:3002BINDING SITE FOR RESIDUE K B 1005
7AC7SOFTWAREALA A:128 , TYR A:132 , ALA B:128 , TYR B:132BINDING SITE FOR RESIDUE SPM B 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XL6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XL6)

(-) Exons   (0, 0)

(no "Exon" information available for 1XL6)

(-) 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:291
 aligned with IRK10_MAGMG | D9N164 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                                                                                                                                                                                                                                                                                                      295      
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    |    - 
          IRK10_MAGMG    11 KPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLMMRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFLVLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQ------   -
               SCOP domains ------------d1xl6a2 A:23-138 Inward rectifier potassium channel kirbac3.1                                                       d1xl6a1 A:139-299 Inward rectifier potassium channel kirbac3.1                                                                                                   -- SCOP domains
               CATH domains --------------------1xl6A01 A:31-138  [code=1.10.287.70, no name defined]                                                       1xl6A02 A:139-301 G protein-activated inward rectifier potassium channel 1                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee......hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeeeee..eeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeee......eeeee..eeeeeee..........hhhhhhhh..eeeeeeeeee....eeeeeeeeee...eee..ee.....................ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xl6 A  11 KPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLMMRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFLVLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQHHHHHH 301
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with IRK10_MAGMG | D9N164 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                                                                                                                                                                                                                                                                                                      295      
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    |    - 
          IRK10_MAGMG    11 KPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLMMRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFLVLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQ------   -
               SCOP domains ------------d1xl6b2 B:23-138 Inward rectifier potassium channel kirbac3.1                                                       d1xl6b1 B:139-299 Inward rectifier potassium channel kirbac3.1                                                                                                   -- SCOP domains
               CATH domains --------------------1xl6B01 B:31-138  [code=1.10.287.70, no name defined]                                                       1xl6B02 B:139-301 G protein-activated inward rectifier potassium channel 1                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeeeee..eeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeee......eeeee..eeeeeee..........hhhhhhhh..eeeeeeeeee....eeeeeeeeee...eee..ee............ee.......ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xl6 B  11 KPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLMMRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFLVLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQHHHHHH 301
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XL6)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IRK10_MAGMG | D9N164)
molecular function
    GO:0005242    inward rectifier potassium channel activity    Enables the transmembrane transfer of a potassium ion by an inwardly-rectifying voltage-gated channel. An inwardly rectifying current-voltage relation is one where at any given driving force the inward flow of K+ ions exceeds the outward flow for the opposite driving force. The inward-rectification is due to a voltage-dependent block of the channel pore by a specific ligand or ligands, and as a result the macroscopic conductance depends on the difference between membrane voltage and the K+ equilibrium potential rather than on membrane voltage itself.
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPM  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xl6)
 
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
  1xl6
    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
  IRK10_MAGMG | D9N164
    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
  IRK10_MAGMG | D9N164
    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
        IRK10_MAGMG | D9N164: 2wlh 2wli 2wlj 2wlk 2wlm 2wln 2wlo 2x6a 2x6b 2x6c 3zrs 4lp8

(-) Related Entries Specified in the PDB File

1xl4 INTERMEDIATE GATING STRUCTURE 1 OF THE SAME PROTEIN