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 :  STRUCTURE OF A MEMBRANE PROTEIN
 
Authors :  H. Takeda, M. Hattori, T. Nishizawa, K. Yamashita, S. T. A. Shah, M. Caff A. D. Maturana, R. Ishitani, O. Nureki
Date :  06 Aug 14  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Channel, Magnesium, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takeda, M. Hattori, T. Nishizawa, K. Yamashita, S. T. Shah, M. Caffrey, A. D. Maturana, R. Ishitani, O. Nureki
Structural Basis For Ion Selectivity Revealed By High-Resolution Crystal Structure Of Mg(2+) Channel Mgte
Nat Commun V. 5 5374 2014
PubMed-ID: 25367295  |  Reference-DOI: 10.1038/NCOMMS6374

(-) Compounds

Molecule 1 - MAGNESIUM TRANSPORTER MGTE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 271-448
    Gene: TTHA1060
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2OLA2Ligand/IonOLEIC ACID
3OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:610 , HOH A:611 , HOH A:612 , HOH B:606 , HOH B:607 , HOH B:608binding site for residue MN A 501
2AC2SOFTWAREGLU A:311 , HOH A:602 , GLU B:275 , GLU B:311binding site for residue MN A 502
3AC3SOFTWARELEU A:349 , TRP A:352 , ARG A:353 , PHE A:410 , TYR B:379binding site for residue OLA A 503
4AC4SOFTWARETYR A:379 , LEU B:349 , TRP B:352 , ARG B:353 , PHE B:410 , ARG B:414binding site for residue OLC A 504
5AC5SOFTWARELEU A:373 , LYS A:377 , TRP A:380 , SER B:301binding site for residue OLC A 505
6AC6SOFTWAREGLN A:304 , HOH A:613 , HOH A:614 , HIS B:383 , HOH B:609 , HOH B:610binding site for residue MN B 501
7AC7SOFTWAREGLU B:307 , GLU B:311 , HOH B:601 , HOH B:603 , HOH B:604 , HOH B:605binding site for residue MN B 502
8AC8SOFTWAREASP A:381 , ARG B:353 , LEU B:357binding site for residue OLC B 504
9AC9SOFTWARELEU A:294 , SER A:301 , ARG A:353 , TRP B:380 , ASP B:381binding site for residue OLC B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U9N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U9N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U9N)

(-) Exons   (0, 0)

(no "Exon" information available for 4U9N)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9n A 272 VYSEAGPVALWLARVRWLVILILTGMVTSSILQGFESVLEAVTALAFYVPVLLGTGGNTGNQSATLIIRALATRDLDLRDWRRVFLKEMGVGLLLGLTLSFLLVGKVYWDGHPLLLPVVGVSLVLIVFFANLVGAMLPFLLRRLGVDPALVSNPLVATLSDVTGLLIYLSVARLLLE 448
                                   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9n B 271 LVYSEAGPVALWLARVRWLVILILTGMVTSSILQGFESVLEAVTALAFYVPVLLGTGGNTGNQSATLIIRALATRDLDLRDWRRVFLKEMGVGLLLGLTLSFLLVGKVYWDGHPLLLPVVGVSLVLIVFFANLVGAMLPFLLRRLGVDPALVSNPLVATLSDVTGLLIYLSVARLLLE 448
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
   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 4U9N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U9N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U9N)

(-) Gene Ontology  (13, 13)

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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ 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 4u9n)
 

(-) 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
  4u9n
    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
  MGTE_THET8 | Q5SMG8
    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
  MGTE_THET8 | Q5SMG8
    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
        MGTE_THET8 | Q5SMG8: 2yvx 2yvy 2yvz 2zy9 4u9l 4wib

(-) Related Entries Specified in the PDB File

4u9l