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 :  CA2+-BOUND MTHK RCK DOMAIN AT 2.5 ANGSTROM
 
Authors :  F. J. Smith, B. S. Rothberg
Date :  13 Jun 13  (Deposition) - 23 Oct 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Regulatory Domain, Calcium Binding, Membrane- Associated, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. J. Smith, V. P. Pau, G. Cingolani, B. S. Rothberg
Structural Basis Of Allosteric Interactions Among Ca(2+)-Binding Sites In A K(+) Channel Rck Domain.
Nat Commun V. 4 2621 2013
PubMed-ID: 24126388  |  Reference-DOI: 10.1038/NCOMMS3621

(-) Compounds

Molecule 1 - CALCIUM-GATED POTASSIUM CHANNEL MTHK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RCK DOMAIN (UNP RESIDUES 107-336)
    Gene: MTHK, MTH_1520
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 187420
    Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NA8Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:184 , GLU A:210 , GLU A:212 , HOH A:505 , HOH A:522 , HOH A:523BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREARG A:241 , ASP A:245 , GLU A:248 , HOH A:504 , GLU B:266BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREGLY A:290 , GLU A:326 , ASP B:305 , HOH B:507 , HOH B:511BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREASP A:287 , HOH A:509 , ASP B:282 , ARG B:308 , HOH B:502BINDING SITE FOR RESIDUE NA A 404
05AC5SOFTWAREASP A:287 , HOH A:511 , HOH A:513 , ASP B:282 , HOH B:506BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWARESER A:137 , GLY A:156 , HOH A:521 , HOH A:530BINDING SITE FOR RESIDUE NA A 406
07AC7SOFTWAREARG A:176 , ASP A:202 , HOH A:542BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWAREASP A:284 , ASP A:287 , HOH A:537 , ASP B:287 , NA B:406BINDING SITE FOR RESIDUE NA A 408
09AC9SOFTWAREASP B:184 , GLU B:210 , GLU B:212 , HOH B:508 , HOH B:510 , HOH B:530BINDING SITE FOR RESIDUE CA B 401
10BC1SOFTWAREASP A:305 , HOH A:506 , GLY B:290 , GLU B:326 , HOH B:501BINDING SITE FOR RESIDUE CA B 402
11BC2SOFTWAREHIS B:161BINDING SITE FOR RESIDUE CL B 403
12BC3SOFTWARESER B:137 , GLY B:156 , HOH B:503 , HOH B:517 , HOH B:533BINDING SITE FOR RESIDUE NA B 404
13BC4SOFTWAREARG B:116 , ARG B:176 , ASP B:202 , HOH B:513 , HOH B:522BINDING SITE FOR RESIDUE NA B 405
14BC5SOFTWARENA A:408 , HOH A:511 , HOH A:537 , ASP B:284 , ASP B:287 , HOH B:506BINDING SITE FOR RESIDUE NA B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L73)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L73)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L73)

(-) Exons   (0, 0)

(no "Exon" information available for 4L73)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains d4l73a1 A:115-244 automated matches                                                                                               d4l73a2 A:245-338 automated matches                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhh....eeeee.hhhhhhhhhh...eeee....hhhhhhhh......eeee...hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..eeehhhhhhhhhhhh....hhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh.eeeeeee..eeee............eeeeeehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l73 A 115 SRHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISALV 338
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334    


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains d4l73b1 B:115-244 automated matches                                                                                               d4l73b2 B:245-336 automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhh....eeeee.hhhhhhhhhhh..eeee....hhhhhhhhh.....eeee...hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeehhhhhhhhhhhh....hhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh.eeeeeee..eeee............eeeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l73 B 115 SRHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISA 336
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L73)

(-) Gene Ontology  (10, 10)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4l73)
 

(-) 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
  4l73
    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
  MTHK_METTH | O27564
    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
  MTHK_METTH | O27564
    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
        MTHK_METTH | O27564: 1lnq 2aef 2aej 2aem 2fy8 2ogu 3kxd 3ldc 3ldd 3lde 3ous 3r65 3rbx 3rbz 4ei2 4hyo 4hz3 4l74 4l75 4l76 4qe7 4qe9 4ro0

(-) Related Entries Specified in the PDB File

4l74 4l75 4l76