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(-) Description

Title :  THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550
 
Authors :  R. Timkovich
Date :  01 Aug 76  (Deposition) - 20 Aug 76  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Timkovich, R. E. Dickerson
The Structure Of Paracoccus Denitrificans Cytochrome C550.
J. Biol. Chem. V. 251 4033 1976
PubMed-ID: 180013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C550
    Chains: A
    Engineered: YES
    Organism Common: MICROCOCCUS DENITRIFICANS
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3UNK13Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , CYS A:18 , HIS A:19 , ILE A:46 , ALA A:47 , TYR A:54 , GLY A:55 , ILE A:58 , TRP A:70 , TYR A:78 , VAL A:79 , PRO A:84 , LYS A:98 , MET A:99 , PHE A:101BINDING SITE FOR RESIDUE HEM A 135

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 155C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 155C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 155C)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY550_PARDE23-139  1A:3-116

(-) Exons   (0, 0)

(no "Exon" information available for 155C)

(-) 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:135
 aligned with CY550_PARDE | P00096 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:136
                                    29        39        49        59        69        79        89        99       109       119       129       139       149      
          CY550_PARDE    20 AQDGDAAKGEKEFNKCKACHMIQAPDGTDIIKGGKTGPNLYGVVGRKIASEEGFKYGEGILEVAEKNPDLTWTEADLIEYVTDPKPWLVKMTDDKGAKTKMTFKMGKNQADVVAFLAQNSPDAGGDGEAAAEGESN 155
               SCOP domains d155ca_ A: Cytochrome c2                                                                                                                 SCOP domains
               CATH domains -155cA00 A:1-134 Cytochrome c                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh.....ee........-......eee.................hhhhhhhhhhh......hhhhhhhhhh........................hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CYTC  PDB: A:3-116 UniProt: 23-139                                                                                   ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 155c A   0 xNEGDAAKGEKEFNKCKACHMIQAPDGTD-IKGGKTGPNLYGVVGRKIASEEGFKYGEGILEVAEKNPDLTWTEANLIEYVTDPKPLVKKMTDDKGAKTKMTFKMGKNQADVVAFLAQDDPDAxxxxxxxxxxxxx 134
                            |        9        19        |-|       38        48        58        68        78        88        98       108       118   ||||128||||||
                            |                          28 |                                                                                          122-UNK||131-UNK
                            0-ACE                        29                                                                                           123-UNK||132-UNK
                                                                                                                                                       124-UNK||133-UNK
                                                                                                                                                        125-UNK| 134-UNK
                                                                                                                                                         126-UNK    
                                                                                                                                                          127-UNK   
                                                                                                                                                           128-UNK  
                                                                                                                                                            129-UNK 
                                                                                                                                                             130-UNK
   Legend:   → Mismatch (orange background)
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  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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 155C)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CY550_PARDE | P00096)
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.

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  155c
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  CY550_PARDE | P00096
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 Related Entries

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

UniProtKB/Swiss-Prot
        CY550_PARDE | P00096: 1cot

(-) Related Entries Specified in the PDB File

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