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(-) Description

Title :  STRUCTURE OF A REDUCED OXYGEN BINDING CYTOCHROME C
 
Authors :  D. Leys, K. Backers, T. E. Meyer, W. R. Hagen, M. A. Cusanovich, J. J. Van Beeumen
Date :  24 Jan 00  (Deposition) - 28 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cytochrome C, Reduced, Disulfide Bridge, Asparagine Ligation, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Leys, K. Backers, T. E. Meyer, W. R. Hagen, M. A. Cusanovich, J. J. Van Beeumen
Crystal Structures Of An Oxygen-Binding Cytochrome C From Rhodobacter Sphaeroides.
J. Biol. Chem. V. 275 16050 2000
PubMed-ID: 10821858  |  Reference-DOI: 10.1074/JBC.275.21.16050
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C
    Chains: A, B, C
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:43 , CYS A:46 , HIS A:47 , ARG A:74 , PHE A:75 , ARG A:80 , VAL A:81 , TRP A:84 , ASN A:88 , VAL A:92 , HOH A:123 , HOH A:140 , HOH A:166 , HOH A:175 , HOH A:224BINDING SITE FOR RESIDUE HEM A 113
2AC2SOFTWARECYS B:43 , CYS B:46 , HIS B:47 , ARG B:74 , PHE B:75 , ARG B:80 , VAL B:81 , TRP B:84 , ASN B:88 , LEU B:105 , HOH B:121 , HOH B:133 , HOH B:179BINDING SITE FOR RESIDUE HEM B 113
3AC3SOFTWARECYS C:43 , CYS C:46 , HIS C:47 , ARG C:58 , ILE C:63 , ARG C:74 , PHE C:75 , ARG C:80 , VAL C:81 , TRP C:84 , ASN C:88 , LEU C:105 , HOH C:136 , HOH C:151 , HOH C:180BINDING SITE FOR RESIDUE HEM C 113

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:89 -A:97
2B:89 -B:97
3C:89 -C:97

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DW3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DW3)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.SHP_RHOS437-129
 
 		  3A:20-112
B:20-112
C:20-112
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.SHP_RHOS437-129
 
 		  1A:20-112
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.SHP_RHOS437-129
 
 		  1-
B:20-112
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.SHP_RHOS437-129
 
 		  1-
-
C:20-112

(-) Exons   (0, 0)

(no "Exon" information available for 1DW3)

(-) Sequences/Alignments

Asymmetric 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 SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw3a_ A: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw3A00 A:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh..........hhhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: A:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw3 A   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw3b_ B: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw3B00 B:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: B:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw3 B   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw3c_ C: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw3C00 C:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: C:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw3 C   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110
   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, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DW3)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SHP_RHOS4 | P81238)
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.

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  1dw3
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  SHP_RHOS4 | P81238
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 Related Entries

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

UniProtKB/Swiss-Prot
        SHP_RHOS4 | P81238: 1dw0 1dw1 1dw2

(-) Related Entries Specified in the PDB File

1dw0 STRUCTURE OF OXIDIZED UNCOMPLEXED SHP
1dw1 STRUCTURE OF CYANIDE COMPLEX OF SHP
1dw2 STRUCTURE OF NITRIC OXIDE COMPLEX OF REDUCED SHP