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(-) Description

Title :  REFINED STRUCTURE OF CYTOCHROME C3 AT 1.8 ANGSTROMS RESOLUTION
 
Authors :  Y. Higuchi, M. Kusunoki, Y. Matsuura, N. Yasuoka, M. Kakudo
Date :  15 Nov 83  (Deposition) - 02 Feb 84  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme Protein Of Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Higuchi, M. Kusunoki, Y. Matsuura, N. Yasuoka, M. Kakudo
Refined Structure Of Cytochrome C3 At 1. 8 A Resolution
J. Mol. Biol. V. 172 109 1984
PubMed-ID: 6319712  |  Reference-DOI: 10.1016/0022-2836(84)90417-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C3
    ChainsA
    EngineeredYES
    Organism ScientificDESULFOVIBRIO VULGARIS
    Organism Taxid881

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:11 , ASP A:12 , LYS A:13 , THR A:14 , GLN A:16 , VAL A:18 , GLY A:39 , TYR A:65 , TYR A:66 , HIS A:70 , CYS A:79 , VAL A:80 , HIS A:83 , LEU A:97 , THR A:98 , GLY A:99 , CYS A:100 , CYS A:105 , HIS A:106 , HOH A:125 , HOH A:131 , HOH A:144 , HOH A:158BINDING SITE FOR RESIDUE HEM A 108
2AC2SOFTWARECYS A:33 , HIS A:35 , ASN A:42 , GLN A:44 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , HIS A:67 , ALA A:68 , THR A:74 , LYS A:75 , PHE A:76 , HOH A:132BINDING SITE FOR RESIDUE HEM A 109
3AC3SOFTWARELYS A:3 , ALA A:4 , PRO A:5 , LEU A:9 , PHE A:20 , HIS A:22 , HIS A:25 , VAL A:28 , LYS A:29 , CYS A:30 , CYS A:33 , HIS A:34 , TYR A:43 , LYS A:45 , CYS A:46 , HEM A:111 , HOH A:150BINDING SITE FOR RESIDUE HEM A 110
4AC4SOFTWAREPHE A:20 , ASN A:21 , THR A:24 , HIS A:25 , CYS A:79 , CYS A:82 , HIS A:83 , LYS A:93 , LYS A:104 , HEM A:110 , HOH A:118 , HOH A:151BINDING SITE FOR RESIDUE HEM A 111

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CDV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CDV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CDV)

(-) Exons   (0, 0)

(no "Exon" information available for 2CDV)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:107
 aligned with CYC3_DESVM | P00132 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:107
                                    33        43        53        63        73        83        93       103       113       123       
           CYC3_DESVM    24 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS 130
               SCOP domains d2cdva_ A: Cytochrome c3                                                                                    SCOP domains
               CATH domains 2cdvA00 A:1-107 Cytochrome C3                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eee............................................hhhhhh.......hhhhhhh........hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2cdv A   1 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKENYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS 107
                                    10        20        30        40        50        60        70        80        90       100       

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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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CDV)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC3_DESVM | P00132)
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:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC3_DESVM | P001321it1 1j0o 1j0p 1wr5 2ewi 2ewk 2ewu 2ffn 2yxc 2yyw 2yyx 2z47

(-) Related Entries Specified in the PDB File

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