Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MEMBRANE PROTEIN FROM CORYNEBACTERIUM DIPHTHERIAE
 
Authors :  R. Zhang, C. Hatzos, S. Clancy, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  12 Feb 08  (Deposition) - 04 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Putative Membrane Protein, Corynebacterium Diphtheriae, Structural Genomics, Psi, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, C. Hatzos, S. Clancy, A. Joachimiak
The Crystal Structure Of A Putative Membrane Protein From Corynebacterium Diphtheriae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MEMBRANE PROTEIN
    Atcc: 700971
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 75-215
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE NCTC 13129
    Organism Taxid: 257309
    Strain: NCTC 13129 / BIOTYPE GRAVIS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3C8I)

(-) Sites  (0, 0)

(no "Site" information available for 3C8I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C8I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C8I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C8I)

(-) Exons   (0, 0)

(no "Exon" information available for 3C8I)

(-) 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:127
 aligned with Q6NIK4_CORDI | Q6NIK4 from UniProtKB/TrEMBL  Length:215

    Alignment length:127
                                    98       108       118       128       138       148       158       168       178       188       198       208       
         Q6NIK4_CORDI    89 DLVPAMIAEVNPRDMVVMALVNTNVDPTLPPRWALATRNITAIPGIEGDTRKVGTRIPAVAVTGQRSVGNQDSWDQISPMPIAWATPDSSVIARAESTIPSEQWTTLSKNLNKLDQVRETKFDLLEL 215
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c8iA00 A:15-141 putative membrane protein from Corynebacterium diphtheriae superfamily                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeee..........eeeeeeee...............eeeeeeee..eee...eee..eeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8i A  15 DLVPAMIAEVNPRDMVVMALVNTNVDPTLPPRWALATRNITAIPGIEGDTRKVGTRIPAVAVTGQRSVGNQDSWDQISPMPIAWATPDSSVIARAESTIPSEQWTTLSKNLNKLDQVRETKFDLLEL 141
                                    24        34        44        54        64        74        84        94       104       114       124       134       


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q6NIK4_CORDI | Q6NIK4 from UniProtKB/TrEMBL  Length:215

    Alignment length:129
                                    96       106       116       126       136       146       156       166       176       186       196       206         
         Q6NIK4_CORDI    87 NYDLVPAMIAEVNPRDMVVMALVNTNVDPTLPPRWALATRNITAIPGIEGDTRKVGTRIPAVAVTGQRSVGNQDSWDQISPMPIAWATPDSSVIARAESTIPSEQWTTLSKNLNKLDQVRETKFDLLEL 215
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c8iB00 B:13-141 putative membrane protein from Corynebacterium diphtheriae superfamily                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeee..........eeeeeeee......hhhhh....eeeeeeeeeee.......eeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8i B  13 NYDLVPAMIAEVNPRDMVVMALVNTNVDPTLPPRWALATRNITAIPGIEGDTRKVGTRIPAVAVTGQRSVGNQDSWDQISPMPIAWATPDSSVIARAESTIPSEQWTTLSKNLNKLDQVRETKFDLLEL 141
                                    22        32        42        52        62        72        82        92       102       112       122       132
   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 3C8I)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C8I)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6NIK4_CORDI | Q6NIK4)
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
(no "Ligands, Modified Residues, Ions" information available for 3c8i)
 
  Sites
(no "Sites" information available for 3c8i)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c8i)
 
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 | Biol. Unit 1 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
  3c8i
    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
  Q6NIK4_CORDI | Q6NIK4
    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
  Q6NIK4_CORDI | Q6NIK4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3C8I)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3C8I)