Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NMR SOLUTION STRUCTURE OF OXIDIZED CYTOCHROME C-553 FROM BACILLUS PASTEURII
 
Authors :  L. Banci, I. Bertini, S. Ciurli, A. Dikiy, J. Dittmer, A. Rosato, G. Sciara, A. R. Thompsett
Date :  03 Oct 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  C-553, Heme, Cytochrome, Bacillus Pasteurii, Electron Transfer, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Banci, I. Bertini, S. Ciurli, A. Dikiy, J. Dittmer, A. Rosato, G. Sciara, A. R. Thompsett
Nmr Solution Structure, Backbone Mobility, And Homology Modeling Of C-Type Cytochromes From Gram-Positive Bacteria.
Chembiochem V. 3 299 2002 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C-553
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC86
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-92
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Synonym: C553

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:31 , CYS A:32 , CYS A:35 , HIS A:36 , ALA A:45 , PRO A:46 , ILE A:48 , TYR A:55 , ILE A:60 , ILE A:63 , ILE A:64 , GLN A:68 , GLY A:69 , GLY A:70 , MET A:71 , ILE A:75 , VAL A:84BINDING SITE FOR RESIDUE HEC A 93

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K3G)

(-) Exons   (0, 0)

(no "Exon" information available for 1K3G)

(-) Sequences/Alignments

NMR Structure
   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:71
 aligned with CY553_SPOPA | P82599 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:71
                                    31        41        51        61        71        81        91 
           CY553_SPOPA   22 VDAEAVVQQKCISCHGGDLTGASAPAIDKAGANYSEEEILDIILNGQGGMPGGIAKGAEAEAVAAWLAEKK 92
               SCOP domains d1k3ga_ A: Cytochrome c6 (synonym: cytochrome c553)                     SCOP domains
               CATH domains 1k3gA00 A:22-92 Cytochrome c                                            CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhh............hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1k3g A 22 VDAEAVVQQKCISCHGGDLTGASAPAIDKAGANYSEEEILDIILNGQGGMPGGIAKGAEAEAVAAWLAEKK 92
                                    31        41        51        61        71        81        91
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K3G)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (CY553_SPOPA | P82599)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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.
    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

NMR Structure
  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
    HEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k3g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  1k3g
    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
  CY553_SPOPA | P82599
    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
  CY553_SPOPA | P82599
    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
        CY553_SPOPA | P82599: 1b7v 1c75 1k3h 1n9c

(-) Related Entries Specified in the PDB File

1c75 1C75 IS THE X-RAY STRUCTURE OF THE CYTOCHROME C553 FROM B. PASTEURII.
1k3h 1K3H IS THE MINIMIZED AVERAGE OF OXIDIZED CYTOCHROME C-553 FROM B. PASTEURII.