Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS
 
Authors :  H. L. Axelrod, G. Feher, J. P. Allen, A. J. Chirino, M. W. Day, B. T. Hsu, D. C. Rees
Date :  14 Feb 94  (Deposition) - 15 Sep 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport (Cytochrome) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Axelrod, G. Feher, J. P. Allen, A. J. Chirino, M. W. Day, B. T. Hsu, D. C. Rees
Crystallization And X-Ray Structure Determination Of Cytochrome C2 From Rhodobacter Sphaeroides In Three Crystal Forms.
Acta Crystallogr. , Sect. D V. 50 596 1994
PubMed-ID: 15299423  |  Reference-DOI: 10.1107/S0907444994001319
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C2
    Chains: A
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063

 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:15 , CYS A:18 , HIS A:19 , THR A:36 , PRO A:38 , ARG A:46 , ALA A:48 , GLY A:49 , TYR A:57 , GLY A:58 , MET A:61 , TRP A:71 , PHE A:76 , TYR A:79 , GLY A:98 , LYS A:99 , MET A:100 , PHE A:102 , HOH A:138 , HOH A:141 , HOH A:142BINDING SITE FOR RESIDUE HEM A 125

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC2_RHOSH3-121  1A:3-121
CYC2_RHOS424-142  1A:3-121

(-) Exons   (0, 0)

(no "Exon" information available for 1CXC)

(-) 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:124
 aligned with CYC2_RHOS4 | Q3J164 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:124
                                    31        41        51        61        71        81        91       101       111       121       131       141    
           CYC2_RHOS4    22 QEGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 145
               SCOP domains d1cxca_ A: Cytochrome c2                                                                                                     SCOP domains
               CATH domains 1cxcA00 A:1-124 Cytochrome c                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh......hhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --CYTC  PDB: A:3-121 UniProt: 24-142                                                                                     --- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cxc A   1 QEGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain A from PDB  Type:PROTEIN  Length:124
 aligned with CYC2_RHOSH | P0C0X8 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           CYC2_RHOSH     1 QEGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
               SCOP domains d1cxca_ A: Cytochrome c2                                                                                                     SCOP domains
               CATH domains 1cxcA00 A:1-124 Cytochrome c                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..ee.....eee............................hhhhhhhh......hhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CYTC  PDB: A:3-121 UniProt: 3-121                                                                                      --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cxc A   1 QEGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 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 1CXC)

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC2_RHOS4 | Q3J164)
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.
    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.
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).

Chain A   (CYC2_RHOSH | P0C0X8)
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.
    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.
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).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cxc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cxc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CYC2_RHOS4 | Q3J164
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CYC2_RHOSH | P0C0X8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CYC2_RHOS4 | Q3J164
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CYC2_RHOSH | P0C0X8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CYC2_RHOS4 | Q3J164: 1cxa 1l9b 1l9j 2cxb
        CYC2_RHOSH | P0C0X8: 1cxa 1l9b 1l9j 2cxb

(-) Related Entries Specified in the PDB File

1cxa 2cxb