Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
(-)Theor. Model - sites
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)
Image Theor. Model - sites
Theor. Model - sites  (Jmol Viewer)

(-) Description

Title :  THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION
 
Authors :  X. Morelli, F. Guerlesquin, M. Czjzek, P. N. Palma
Date :  08 Dec 99  (Deposition) - 10 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR; THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B  (3x)
Keywords :  Electron Transfer, Ferredoxin-Cytochrome Complex, Model, Heteronuclear Nmr, Docking (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Morelli, A. Dolla, M. Czjzek, P. N. Palma, F. Blasco, L. Krippahl, J. J. G. Moura, F. Guerlesquin
Heteronuclear Nmr And Soft Docking: An Experimental Approach For A Structural Model Of The Cytochrome C553-Ferredoxin Complex
Biochemistry V. 39 2530 2000
PubMed-ID: 10704202  |  Reference-DOI: 10.1021/BI992306S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN I
    Cellular LocationPERIPLASM
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    GeneFDXI
    Organism ScientificDESULFOMICROBIUM NORVEGICUM
    Organism Taxid52561
    Other DetailsCONTAINS A FE4S4 CLUSTER COVALENTLY LINKED BY FOUR CYSTEINS
    PlasmidPETFDI
 
Molecule 2 - CYTOCHROME C553
    Cellular LocationCYTOPLASM
    ChainsB
    Organism ScientificDESULFOVIBRIO VULGARIS
    Organism Taxid882
    Other DetailsCONTAINS A HEME GROUP COVALENTLY LINKED BY 2 CYSTEINES AND THE IRON ATOM IS COORDINATED BY A HISTIDINE AND A METHIONINE
    StrainHILDENBOROUGH
    SynonymLOW POTENTIAL CYTOCHROME C

 Structural Features

(-) Chains, Units

  
Theoretical Model (3x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Theoretical Model (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:4 , CYS A:9 , GLY A:11 , CYS A:12 , GLU A:13 , SER A:14 , CYS A:15 , ASP A:27 , ALA A:47 , ALA A:50 , CYS A:51 , PRO A:52BINDING SITE FOR RESIDUE SF4 A 60
2AC2SOFTWARECYS A:12 , SER A:14 , TYR B:7 , CYS B:10 , CYS B:13 , HIS B:14 , MET B:23 , ALA B:26 , LYS B:27 , VAL B:29 , LEU B:37 , LYS B:40 , MET B:41 , TYR B:44 , TYR B:49 , GLY B:51 , GLU B:52 , ARG B:53 , LYS B:54 , MET B:56 , MET B:57 , TYR B:64 , LEU B:72 , MET B:76BINDING SITE FOR RESIDUE HEC B 80

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER1_DESNO1-28  1A:1-28
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER1_DESNO9-20  1A:9-20

(-) Exons   (0, 0)

(no "Exon" information available for 1DWL)

(-) Sequences/Alignments

Theoretical Model
   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:59
 aligned with FER1_DESNO | P07485 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:59
                                    10        20        30        40        50         
           FER1_DESNO     1 TIVIDHEECIGCESCVELCPEVFAMIDGEEKAMVTAPDSTAECAQDAIDACPVEAISKE  59
               SCOP domains d1dwla_ A: Ferredoxin-cytochrome complex                    SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........hhhhhh....eeeee....eee......hhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: A:1-28    ------------------------------- PROSITE (1)
                PROSITE (2) --------4FE4S_FER_1 --------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 1dwl A   1 TIVIDHEECIGCESCVELCPEVFAMIDGEEKAMVTAPDSTAECAQDAIDACPVEAISKE  59
                                    10        20        30        40        50         

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with CY553_DESVH | P04032 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:79
                                    34        44        54        64        74        84        94         
          CY553_DESVH    25 ADGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL 103
               SCOP domains d1dwlb_ B: Ferredoxin-cytochrome complex                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhh.................hhhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1dwl B   1 ADGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL  79
                                    10        20        30        40        50        60        70         

   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, 2)

Theoretical Model

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 11)

Theoretical Model(hide GO term definitions)
Chain A   (FER1_DESNO | P07485)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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.

Chain B   (CY553_DESVH | P04032)
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: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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

Theoretical Model
  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 ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dwl)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1dwl
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CY553_DESVH | P04032
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  FER1_DESNO | P07485
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CY553_DESVH | P04032
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  FER1_DESNO | P07485
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CY553_DESVH | P040321dvh 1e08 2dvh

(-) Related Entries Specified in the PDB File

1dvh CYTOCHROME C553 (REDUCED) (NMR, 36 STRUCTURES)
1fxd FERREDOXIN II OF DESULFOVIBRIO GIGAS (CRYSTAL STRUCTURE)
2dvh THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES