1DW1 - JenaLib

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Title :   STRUCTURE OF THE CYANIDE COMPLEX OF SHP, AN 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 :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Cytochrome C, Cyanide Complex, 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)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CYN	3	Ligand/Ion	CYANIDE ION
2	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CYN	1	Ligand/Ion	CYANIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CYN	1	Ligand/Ion	CYANIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CYN	1	Ligand/Ion	CYANIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:84 , ASN A:88 , HEM A:113	BINDING SITE FOR RESIDUE CYN A 114
2	AC2	SOFTWARE	TRP B:84 , ASN B:88 , HEM B:113	BINDING SITE FOR RESIDUE CYN B 114
3	AC3	SOFTWARE	TRP C:84 , LEU C:85 , ASN C:88 , HEM C:113	BINDING SITE FOR RESIDUE CYN C 114
4	AC4	SOFTWARE	CYS A:43 , CYS A:46 , HIS A:47 , LEU A:66 , ARG A:74 , PHE A:75 , ARG A:80 , VAL A:81 , TRP A:84 , ASN A:88 , VAL A:92 , CYN A:114 , HOH A:124 , HOH A:141 , HOH A:165 , HOH A:173 , HOH A:201	BINDING SITE FOR RESIDUE HEM A 113
5	AC5	SOFTWARE	CYS B:43 , CYS B:46 , HIS B:47 , ILE B:63 , ARG B:74 , PHE B:75 , ARG B:80 , VAL B:81 , TRP B:84 , ASN B:88 , VAL B:92 , CYN B:114 , HOH B:123 , HOH B:135 , HOH B:175	BINDING SITE FOR RESIDUE HEM B 113
6	AC6	SOFTWARE	CYS 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 , VAL C:92 , CYN C:114 , HOH C:131 , HOH C:146 , HOH C:171	BINDING SITE FOR RESIDUE HEM C 113

Asymmetric Unit

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

(no "Cis Peptide Bond" information available for 1DW1)

(no "SAP(SNP)/Variant" information available for 1DW1)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	3	A:20-112 B:20-112 C:20-112

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	A:20-112 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	- B:20-112 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	- - C:20-112

(no "Exon" information available for 1DW1)

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 d1dw1a_ A: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw1A00 A: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: A:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw1 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 d1dw1b_ B: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw1B00 B: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: B:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw1 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 d1dw1c_ C: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw1C00 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
                 1dw1 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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: SHP, an oxygen binding cytochrome c (4)

Rhodobacter sphaeroides [TaxId: 1063] (4)

1a	d1dw1a_	A:
1b	d1dw1b_	B:
1c	d1dw1c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Rhodobacter sphaeroides. Organism_taxid: 1063 (7)

1a	1dw1A00	A:1-112
1b	1dw1B00	B:1-112
1c	1dw1C00	C:1-112

(no "Pfam Domain" information available for 1DW1)

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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dw1)

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	SHP_RHOS4 \| P81238	:	1dw0 1dw2 1dw3

1dw0	STRUCTURE OF OXIDIZED UNCOMPLEXED SHP
1dw2	STRUCTURE OF NITRIC OXIDE COMPLEX OF REDUCED SHP
1dw3	STRUCTURE OF REDUCED SHP

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