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(-) Description

Title :  CYTOCHROME C' FROM RHODOBACTER SPHERIODES
 
Authors :  K. A. Kantardjieff, B. Rupp
Date :  22 Nov 01  (Deposition) - 19 Dec 02  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Electron Transport, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Ramirez, H. L. Axelrod, S. R. Herron, B. Rupp, J. P. Allen, K. A. Kantardjieff
High Resolution Crystal Structure Of Ferricytochrome C' Fro Rhodobacter Sphaeroides
J. Chem. Cryst. V. 33 413 2003
PubMed: search

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Atcc: 17023
    Cellular Location: PERIPLASMIC
    Chains: A, D
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: FERRICYTOCHROME C'

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , LYS A:11 , PHE A:14 , THR A:70 , ALA A:71 , ALA A:72 , PHE A:90 , CYS A:119 , CYS A:122 , HIS A:123 , ARG A:127 , HOH A:2156 , GLU D:8BINDING SITE FOR RESIDUE HEC A 131
2AC2SOFTWAREARG D:10 , LYS D:11 , PHE D:14 , SER D:15 , THR D:70 , ALA D:71 , PHE D:83 , PHE D:90 , CYS D:119 , CYS D:122 , HIS D:123 , ARG D:127 , HOH D:2135BINDING SITE FOR RESIDUE HEC D 131

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_RHOS424-147
 		  2A:5-128
D:5-128

(-) Exons   (0, 0)

(no "Exon" information available for 1GQA)

(-) 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:130
 aligned with CYCP_RHOS4 | P00148 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
           CYCP_RHOS4    20 ADAEHVVEARKGYFSLVALEFGPLAAMAKGEMPYDAAAAKAHASDLVTLTKYDPSDLYAPGTSADDVKGTAAKAAIWQDADGFQAKGMAFFEAVAALEPAAGAGQKELAAAVGKVGGTCKSCHDDFRVKR 149
               SCOP domains d1gqaa_ A: Cytochrome c'                                                                                                           SCOP domains
               CATH domains 1gqaA00 A:1-130  [code=1.20.120.10, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----CYTCII  PDB: A:5-128 UniProt: 24-147                                                                                        -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gqa A   1 ADAEHVVEARKGYFSLVALEFGPLAAMAKGEMPYDAAAAKAHASDLVTLTKYDPSDLYAPGTSADDVKGTAAKAAIWQDADGFQAKGMAFFEAVAALEPAAGAGQKELAAAVGKVGGTCKSCHDDFRVKR 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with CYCP_RHOS4 | P00148 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
           CYCP_RHOS4    20 ADAEHVVEARKGYFSLVALEFGPLAAMAKGEMPYDAAAAKAHASDLVTLTKYDPSDLYAPGTSADDVKGTAAKAAIWQDADGFQAKGMAFFEAVAALEPAAGAGQKELAAAVGKVGGTCKSCHDDFRVKR 149
               SCOP domains d1gqad_ D: Cytochrome c'                                                                                                           SCOP domains
               CATH domains 1gqaD00 D:1-130  [code=1.20.120.10, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----CYTCII  PDB: D:5-128 UniProt: 24-147                                                                                        -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gqa D   1 ADAEHVVEARKGYFSLVALEFGPLAAMAKGEMPYDAAAAKAHASDLVTLTKYDPSDLYAPGTSADDVKGTAAKAAIWQDADGFQAKGMAFFEAVAALEPAAGAGQKELAAAVGKVGGTCKSCHDDFRVKR 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (CYCP_RHOS4 | P00148)
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:0022900    electron transport chain    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: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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