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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF MNTC FROM SYNECHOCYSTIS 6803
 
Authors :  V. Rukhman, R. Anati, M. Melamed-Frank, M. Bhattacharyya-Pakrasi, H. B. Pakrasi, N. Adir
Date :  28 Oct 04  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Manganese, Abc-Type Transport Systems, Photosynthesis, Cyanobacteria, Disulfide Bond, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Rukhman, R. Anati, M. Melamed-Frank, N. Adir
The Mntc Crystal Structure Suggests That Import Of Mn2+ In Cyanobacteria Is Redox Controlled.
J. Mol. Biol. V. 348 961 2005
PubMed-ID: 15843026  |  Reference-DOI: 10.1016/J.JMB.2005.03.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MN TRANSPORTER
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3XC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 10-330
    Gene: MNTC
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6803
    Organism Taxid: 1148
    Synonym: MNTC PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , HIS A:154 , GLU A:220 , ASP A:295BINDING SITE FOR RESIDUE MN A 900
2AC2SOFTWAREHIS B:89 , HIS B:154 , GLU B:220 , ASP B:295BINDING SITE FOR RESIDUE MN B 900
3AC3SOFTWAREHIS C:89 , HIS C:154 , GLU C:220 , ASP C:295BINDING SITE FOR RESIDUE MN C 900

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:219 -A:268
2B:219 -B:268
3C:219 -C:268

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XVL)

(-) 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:279
 aligned with Q79EF9_SYNY3 | Q79EF9 from UniProtKB/TrEMBL  Length:330

    Alignment length:279
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         
         Q79EF9_SYNY3    49 GETEEKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEYDARVITNGLLAGTN 327
               SCOP domains d1xvla1 A:49-327 Mn transporter MntC                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.hhhhhhhhhhhhh...eeee.............hhhhhhhhhh..eeee.......hhhhhhhh.....eee.....................hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhh..eeeeee........hhhhhhhhhhhhhh....eeeee....hhhhhhhhh....eeeeee.............hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvl A  49 GETEEKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEYDARVITNGLLAGTN 327
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q79EF9_SYNY3 | Q79EF9 from UniProtKB/TrEMBL  Length:330

    Alignment length:271
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322 
         Q79EF9_SYNY3    53 EKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEYDARVITNGLL 323
               SCOP domains d1xvlb_ B: Mn transporter MntC                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhhhh...eeee.............hhhhhhhhhh..eeee.......hhhhhhh......eee.....................hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhh.eeeeee..hhhhhhhh..eeeeee........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvl B  53 EKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEYDARVITNGLL 323
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322 


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with Q79EF9_SYNY3 | Q79EF9 from UniProtKB/TrEMBL  Length:330

    Alignment length:262
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
         Q79EF9_SYNY3    52 EEKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEY 313
               SCOP domains d1xvlc_ C: Mn transporter MntC                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SBP_bac_9-1xvlC01 C:57-313                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -----SBP_bac_9-1xvlC02 C:57-313                                                                                                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) -----SBP_bac_9-1xvlC03 C:57-313                                                                                                                                                                                                                                        Pfam domains (3)
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhheeee.............hhhhhhhhh...eeee.......hhhhhhhhh....eee............----.....hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh-------------------.hhhhhhhhhh.-------.........hhhhhhhhhhhhhhh..............---------------...............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvl C  52 EEKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIAD----DKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAID-------------------CEGAFSYLARDY-------WPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDK---------------NLYVDSLSTEEGPVPTFLDLLEY 313
                                    61        71        81        91       101       111       121       131       141  |    151       161       171       181       191       | -         -       221        |-      |241       251       261       271   |     -       291       301       311  
                                                                                                                      144  149                                               199                 219        230     238                                  275             291
   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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XVL)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: SBP_bac_9] (16)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q79EF9_SYNY3 | Q79EF9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xvl)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  1xvl
    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
  Q79EF9_SYNY3 | Q79EF9
    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
  Q79EF9_SYNY3 | Q79EF9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q79EF9_SYNY3 | Q79EF9: 3ujp 4irm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XVL)