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(-) Description

Title :  CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
 
Authors :  P. Simoes, P. M. Matias, J. Morais, K. Wilson, Z. Dauter, M. A. Carrondo
Date :  18 Jun 97  (Deposition) - 24 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Simoes, P. M. Matias, J. Morais, K. Wilson, Z. Dauter, M. A. Carrondo
Refinement Of The Three-Dimensional Structures Of Cytochromes C3 From Desulfovibrio Vulgaris Hildenborough At 1. 67 Angstrom Resolution And From Desulfovibrio Desulfuricans Atcc 27774 At 1. 6 Angstrom Resolution
Inorg. Chim. Acta. V. 273 213 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C3
    ChainsA, B
    Organism ScientificDESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH
    Organism Taxid882
    StrainHILDENBOROUGH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:11 , GLU A:12 , ALA A:13 , THR A:14 , GLN A:16 , PRO A:17 , VAL A:18 , TYR A:65 , TYR A:66 , HIS A:70 , CYS A:79 , HIS A:83 , LEU A:97 , GLY A:99 , CYS A:100 , CYS A:105 , HIS A:106 , HOH A:253 , HOH A:324 , HOH A:334 , HOH A:338BINDING SITE FOR RESIDUE HEM A 109
2AC2SOFTWARELYS A:10 , CYS A:33 , HIS A:35 , ARG A:44 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , HIS A:67 , THR A:74 , LYS A:75 , PHE A:76 , HOH A:305BINDING SITE FOR RESIDUE HEM A 110
3AC3SOFTWAREPRO A:2 , PRO A:5 , PHE A:20 , HIS A:22 , HIS A:25 , VAL A:28 , CYS A:30 , CYS A:33 , HIS A:34 , LYS A:45 , CYS A:46 , HEM A:112 , HOH A:240 , HOH A:297 , HOH A:342BINDING SITE FOR RESIDUE HEM A 111
4AC4SOFTWAREASN A:21 , THR A:24 , HIS A:25 , SER A:78 , CYS A:79 , CYS A:82 , HIS A:83 , LYS A:104 , HEM A:111 , HOH A:231 , HOH A:318BINDING SITE FOR RESIDUE HEM A 112
5AC5SOFTWAREMET B:11 , GLU B:12 , ALA B:13 , THR B:14 , GLN B:16 , PRO B:17 , TYR B:65 , TYR B:66 , HIS B:70 , CYS B:79 , HIS B:83 , LEU B:97 , THR B:98 , GLY B:99 , CYS B:100 , CYS B:105 , HIS B:106 , HOH B:270 , HOH B:315BINDING SITE FOR RESIDUE HEM B 109
6AC6SOFTWAREALA A:1 , LYS B:10 , HIS B:35 , VAL B:37 , ARG B:44 , CYS B:46 , CYS B:51 , HIS B:52 , HIS B:67 , THR B:74 , LYS B:75 , PHE B:76 , HOH B:309 , HOH B:327 , HOH B:335BINDING SITE FOR RESIDUE HEM B 110
7AC7SOFTWAREHOH A:300 , PRO B:5 , PHE B:20 , HIS B:22 , HIS B:25 , VAL B:28 , CYS B:30 , CYS B:33 , HIS B:34 , TYR B:43 , LYS B:45 , CYS B:46 , HEM B:112 , HOH B:284 , HOH B:341BINDING SITE FOR RESIDUE HEM B 111
8AC8SOFTWAREASN B:21 , THR B:24 , HIS B:25 , CYS B:79 , CYS B:82 , HIS B:83 , LYS B:104 , HEM B:111 , HOH B:229 , HOH B:282 , HOH B:299BINDING SITE FOR RESIDUE HEM B 112

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CTH)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC3_DESVH47-110
 
  2A:25-88
B:25-88
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC3_DESVH47-110
 
  1A:25-88
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC3_DESVH47-110
 
  1-
B:25-88

(-) Exons   (0, 0)

(no "Exon" information available for 2CTH)

(-) 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:107
 aligned with CYC3_DESVH | P00131 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:107
                                    32        42        52        62        72        82        92       102       112       122       
           CYC3_DESVH    23 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 129
               SCOP domains d2ctha_ A: Cytochrome c3                                                                                    SCOP domains
               CATH domains 2cthA00 A:1-107 Cytochrome C3                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eee..hhh....hhh................................hhhhhh........hhhhhhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------MULTIHEME_CYTC  PDB: A:25-88 UniProt: 47-110                    ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2cth A   1 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 107
                                    10        20        30        40        50        60        70        80        90       100       

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with CYC3_DESVH | P00131 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:107
                                    32        42        52        62        72        82        92       102       112       122       
           CYC3_DESVH    23 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 129
               SCOP domains d2cthb_ B: Cytochrome c3                                                                                    SCOP domains
               CATH domains 2cthB00 B:1-107 Cytochrome C3                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eee..hhh....hhh................................hhhhhh........hhhhhhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------MULTIHEME_CYTC  PDB: B:25-88 UniProt: 47-110                    ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2cth B   1 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 107
                                    10        20        30        40        50        60        70        80        90       100       

   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)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYC3_DESVH | P00131)
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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UniProtKB/Swiss-Prot
        CYC3_DESVH | P001311a2i 1gx7 1mdv 2bpn 2cym

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