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

(-) Description

Title :  PSII ASSOCIATED CYTOCHROME C549 FROM SYNECHOCYSTIS SP.
 
Authors :  C. Frazao, F. J. Enguita, R. Coelho, G. M. Sheldrick
Date :  19 May 00  (Deposition) - 04 May 01  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Psii Associated Cytochrome, Cytochrome, Low Potential, Bis_histidinyl, Psii Modulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Frazao, F. J. Enguita, R. Coelho, G. M. Sheldrick, J. A. Navarro, M. Hervas, M. A. De La Rosa, M. A. Carrondo
Crystal Structure Of Low-Potential Cytochrome C549 From Synechocystis Sp. Pcc 6803 At 1. 21A Resolution
J. Biol. Inorg. Chem. V. 6 324 2001
PubMed-ID: 11315568  |  Reference-DOI: 10.1007/S007750100208

(-) Compounds

Molecule 1 - CYTOCHROME C549
    Chains: A
    Organism Scientific: SYNECHOCYSTIS SP
    Organism Taxid: 1143
    Strain: PCC 6803

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2HEC1Ligand/IonHEME C

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:49 , ASN A:50 , HOH A:509 , HOH A:442 , HOH A:444 , HOH A:415 , HOH A:361 , HOH A:374BINDING SITE FOR RESIDUE CA Z 225
2AC2SOFTWAREASP A:35 , GLU A:127 , HOH A:449 , HOH A:332 , HOH A:451 , HOH A:371BINDING SITE FOR RESIDUE CA Z 226
3AC3SOFTWAREASP A:35 , HOH A:499 , HOH A:514 , HOH A:449 , HOH A:308 , HOH A:461 , HOH A:340 , HOH A:393BINDING SITE FOR RESIDUE CA Z 227
4AC4SOFTWARETHR A:36 , CYS A:37 , CYS A:40 , HIS A:41 , THR A:48 , ASN A:49 , VAL A:52 , SER A:53 , LEU A:54 , ASP A:58 , LEU A:59 , ALA A:62 , ARG A:66 , LEU A:72 , PHE A:75 , TYR A:82 , GLU A:90 , HIS A:92 , HOH A:362 , HOH A:406 , HOH A:319BINDING SITE FOR RESIDUE HEC A 136

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E29)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:63 -Pro A:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E29)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY550_SYNY349-148  1A:24-123

(-) Exons   (0, 0)

(no "Exon" information available for 1E29)

(-) 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:135
 aligned with CY550_SYNY3 | Q55013 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:135
                                    35        45        55        65        75        85        95       105       115       125       135       145       155     
          CY550_SYNY3    26 VELTESTRTIPLDEAGGTTTLTARQFTNGQKIFVDTCTQCHLQGKTKTNNNVSLGLADLAGAEPRRDNVLALVEFLKNPKSYDGEDDYSELHPNISRPDIYPEMRNYTEDDIFDVAGYTLIAPKLDERWGGTIYF 160
               SCOP domains d1e29a_ A: Photosystem II associated cytochrome c549                                                                                    SCOP domains
               CATH domains 1e29A00 A:1-135 Cytochrome c                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eee.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhh......................hhhhh..hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------CYTC  PDB: A:24-123 UniProt: 49-148                                                                 ------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e29 A   1 VELTESTRTIPLDEAGGTTTLTARQFTNGQKIFVDTCTQCHLQGKTKTNNNVSLGLADLAGAEPRRDNVLALVEFLKNPKSYDGEDDYSELHPNISRPDIYPEMRNYTEDDIFDVAGYTLIAPKLDERWGGTIYF 135
                                    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, 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 1E29)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CY550_SYNY3 | Q55013)
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:0018063    cytochrome c-heme linkage    The linkage of cytochromes and other heme proteins to heme.
    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:0019684    photosynthesis, light reaction    The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
    GO:0022904    respiratory electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009523    photosystem II    A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center.
    GO:0030096    plasma membrane-derived thylakoid photosystem II    A protein complex, located in the membrane-derived thylakoid, containing the P680 reaction center. In the light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:63 - Pro A:64   [ RasMol ]  
 

(-) 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
  1e29
    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
  CY550_SYNY3 | Q55013
    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
  CY550_SYNY3 | Q55013
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1E29)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1E29)