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(-) Description

Title :  REFINEMENT OF THE CRYSTAL STRUCTURE OF OXIDIZED RHODOSPIRILLUM RUBRUM CYTOCHROME C2
 
Authors :  G. Bhatia, B. C. Finzel, J. Kraut
Date :  03 Nov 83  (Deposition) - 02 Feb 84  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport Protein (Cytochrome) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. E. Bhatia
Refinement Of The Crystal Structure Of Oxidized Rhodospirillum Rubrum Cytochrome C2
Thesis 1981
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C2
    Chains: A
    Engineered: YES
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Organism Taxid: 1085

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:14 , CYS A:17 , HIS A:18 , ALA A:40 , ALA A:41 , HIS A:42 , TYR A:46 , TYR A:48 , SER A:49 , TYR A:52 , TRP A:62 , TYR A:70 , SER A:89 , LYS A:90 , MET A:91 , PHE A:93BINDING SITE FOR RESIDUE HEM A 113

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C2C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C2C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C2C)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC2_RHORU2-112  1A:2-112
CYC2_RHORT25-135  1A:2-112

(-) Exons   (0, 0)

(no "Exon" information available for 2C2C)

(-) 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:112
 aligned with CYC2_RHORT | Q2RVM4 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:112
                                    33        43        53        63        73        83        93       103       113       123       133  
           CYC2_RHORT    24 EGDAAAGEKVSKKCLACHTFDQGGANKVGPNLFGVFENTAAHKDDYAYSESYTEMKAKGLTWTEANLAAYVKDPKAFVLEKSGDPKAKSKMTFKLTKDDEIENVIAYLKTLK 135
               SCOP domains d2c2ca_ A: Cytochrome c2                                                                                         SCOP domains
               CATH domains 2c2cA00 A:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...............................hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -CYTC  PDB: A:2-112 UniProt: 25-135                                                                              PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2c2c A   1 EGDAAAGEKVSKKCLACHTFDQGGANKVGPNLFGVFENTAAHKDNYAYSESYTEMKAKGLTWTEANLAAYVKNPKAFVLEKSGDPKAKSKMTFKLTKDDEIENVIAYLKTLK 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain A from PDB  Type:PROTEIN  Length:112
 aligned with CYC2_RHORU | P0C189 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           CYC2_RHORU     1 EGDAAAGEKVSKKCLACHTFDQGGANKVGPNLFGVFENTAAHKDNYAYSESYTEMKAKGLTWTEANLAAYVKNPKAFVLEKSGDPKAKSKMTFKLTKDDEIENVIAYLKTLK 112
               SCOP domains d2c2ca_ A: Cytochrome c2                                                                                         SCOP domains
               CATH domains 2c2cA00 A:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...............................hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: A:2-112 UniProt: 2-112                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2c2c A   1 EGDAAAGEKVSKKCLACHTFDQGGANKVGPNLFGVFENTAAHKDNYAYSESYTEMKAKGLTWTEANLAAYVKNPKAFVLEKSGDPKAKSKMTFKLTKDDEIENVIAYLKTLK 112
                                    10        20        30        40        50        60        70        80        90       100       110
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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 2C2C)

(-) Gene Ontology  (8, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC2_RHORU | P0C189)
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:0045154    electron transporter, transferring electrons within cytochrome c oxidase complex activity    Enables the directed movement of electrons within the cytochrome c oxidase complex.
    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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.

Chain A   (CYC2_RHORT | Q2RVM4)
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: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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0009767    photosynthetic electron transport chain    A process, occurring as part of photosynthesis, in which light provides the energy for a series of electron carriers to operate together to transfer electrons and generate a transmembrane electrochemical gradient.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC2_RHORT | Q2RVM4: 3c2c
        CYC2_RHORU | P0C189: 3c2c

(-) Related Entries Specified in the PDB File

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