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(-)Theoretical Model
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Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODELED COMPLEX BETWEEN PHOTOSYSTEM II AND CYTOCHROME C549
 
Authors :  C. A. Kerfeld, M. R. Sawaya, T. O. Yeates, D. W. Krogmann
Date :  17 Apr 01  (Deposition) - 08 Aug 01  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E,F,G,H,I,J,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Theoretical Model Of Photosystem Ii With The Dimeric Cytochrome C549 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Sawaya, D. W. Krogmann, A. Serag, K. K. Ho, T. O. Yeates, C. A. Kerfeld
Structures Of Cytochrome C-549 And Cytochrome C6 From The Cyanobacterium Arthrospira Maxima.
Biochemistry V. 40 9215 2001
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Cellular Location: THYLAKOID MEMBRANE
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 2
    Cellular Location: THYLAKOID MEMBRANE
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 3
    Cellular Location: THYLAKOID MEMBRANE
    Chains: C
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 4
    Cellular Location: THYLAKOID MEMBRANE
    Chains: D
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 5
    Cellular Location: THYLAKOID MEMBRANE
    Chains: E
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 6
    Cellular Location: THYLAKOID MEMBRANE
    Chains: F
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 7
    Cellular Location: THYLAKOID MEMBRANE
    Chains: G
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 8
    Cellular Location: THYLAKOID MEMBRANE, LUMEN
    Chains: H
    Organism Common: BACTERIA
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
 
Molecule 9
    Cellular Location: THYLAKOID MEMBRANE, LUMEN
    Chains: I, J
    Organism Common: BACTERIA
    Organism Scientific: ARTHROSPIRA MAXIMA

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 1197)

Theoretical Model (9, 1197)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2CLA32Ligand/IonCHLOROPHYLL A
3FE1Ligand/IonFE (III) ION
4HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5MN4Ligand/IonMANGANESE (II) ION
6PHO2Ligand/IonPHEOPHYTIN A
7PLA1Ligand/Ion2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
8TYR2Mod. Amino AcidTYROSINE
9UNK1151Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 1IGK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Theoretical Model
No.Residues
1Thr I:63 -Pro I:64
2Thr J:63 -Pro J:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Theoretical Model (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY550_ARTMA22-121
 		  2I:24-123
J:24-123

(-) Exons   (0, 0)

(no "Exon" information available for 1IGK)

(-) Sequences/Alignments

Theoretical Model
   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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1igk A   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 169
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Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1igk B   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 174
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Chain C from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1igk C   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 156
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Chain D from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1igk D   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 155
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Chain E from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ........................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 1igk E   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  40
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Chain F from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1igk F   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  30
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Chain G from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................................................................................................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1igk G   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 312
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Chain H from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1igk H   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 115
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Chain I from PDB  Type:PROTEIN  Length:129
 aligned with CY550_ARTMA | P82603 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          CY550_ARTMA     1 LTEELRTFPINAQGDTAVLSLKEIKKGQQVFNAACAQCHALGVTRTNPDVNLSPEALALATPPRDNIAALVDYIKNPTTYDGFVEISELHPSLKSSDIFPKMRNISEDDLYNVAGYILLQPKVRGEQWG 129
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhh......................hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------CYTC  PDB: I:24-123 UniProt: 22-121                                                                 -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1igk I   3 LTEELRTFPINAQGDTAVLSLKEIKKGQQVFNAACAQCHALGVTRTNPDVNLSPEALALATPPRDNIAALVDYIKNPTTYDGFVEISELHPSLKSSDIFPKMRNISEDDLYNVAGYILLQPKVRGEQWG 131
                                    12        22        32        42        52        62        72        82        92       102       112       122         


Chain J from PDB  Type:PROTEIN  Length:129
 aligned with CY550_ARTMA | P82603 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
          CY550_ARTMA     1 LTEELRTFPINAQGDTAVLSLKEIKKGQQVFNAACAQCHALGVTRTNPDVNLSPEALALATPPRDNIAALVDYIKNPTTYDGFVEISELHPSLKSSDIFPKMRNISEDDLYNVAGYILLQPKVRGEQWG 129
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhh......................hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------CYTC  PDB: J:24-123 UniProt: 22-121                                                                 -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1igk J   3 LTEELRTFPINAQGDTAVLSLKEIKKGQQVFNAACAQCHALGVTRTNPDVNLSPEALALATPPRDNIAALVDYIKNPTTYDGFVEISELHPSLKSSDIFPKMRNISEDDLYNVAGYILLQPKVRGEQWG 131
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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  (0, 0)

(no "SCOP Domain" information available for 1IGK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1IGK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Theoretical Model(hide GO term definitions)
Chain I,J   (CY550_ARTMA | P82603)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CY550_ARTMA | P82603: 1f1c

(-) Related Entries Specified in the PDB File

1f1c CYTOCHROME C549 DIMER
1fe1 PHOTOSYSTEM II