1VYD - JenaLib

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Title :   CRYSTAL STRUCTURE OF CYTOCHROME C2 MUTANT G95E

Authors :   C. Dumortier, J. Fitch, F. Van Petegem, W. Vermeulen, T. E. Meyer, J. J. Van Beeumen, M. A. Cusanovich

Date :   27 Apr 04 (Deposition) - 17 Jun 04 (Release) - 20 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Electron Transport, Redox (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Dumortier, J. Fitch, F. Van Petegem, W. Vermeulen, T. E. Meyer, J. J. Van Beeumen, M. A. Cusanovich
Protein Dynamics In The Region Of The Sixth Ligand Methionine Revealed By Studies Of Imidazole Binding To Rhodobacter Capsulatus Cytochrome C2 Hinge Mutants.
Biochemistry V. 43 7717 2004
PubMed-ID: 15196014 | Reference-DOI: 10.1021/BI0362370

Molecule 1 - CYTOCHROME C2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	RHODOBACTER CAPSULATUS
	Organism Taxid	:	1061

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:12 , CYS A:13 , CYS A:16 , HIS A:17 , LEU A:37 , ARG A:43 , ALA A:45 , GLY A:46 , TYR A:53 , LYS A:54 , ILE A:57 , TRP A:67 , TYR A:75 , VAL A:76 , GLU A:95 , MET A:96 , PHE A:98 , HOH A:2017 , HOH A:2028 , HOH A:2038 , HOH A:2039	BINDING SITE FOR RESIDUE HEM A1117
2	AC2	SOFTWARE	CYS B:13 , CYS B:16 , HIS B:17 , ARG B:43 , ALA B:45 , GLY B:46 , TYR B:53 , LYS B:54 , ILE B:57 , TRP B:67 , TYR B:75 , VAL B:76 , THR B:94 , GLU B:95 , MET B:96 , PHE B:98 , HOH B:2043	BINDING SITE FOR RESIDUE HEM B1117

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

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

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYC2_RHOCB_001 *	L	108	T	CYC2_RHOCB	---	---	A/B	L	87	T
2	UniProt	VAR_CYC2_RHOCB_002 *	T	115	S	CYC2_RHOCB	---	---	A/B	T	94	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYC2_RHOCB_001 *	L	108	T	CYC2_RHOCB	---	---	A	L	87	T
2	UniProt	VAR_CYC2_RHOCB_002 *	T	115	S	CYC2_RHOCB	---	---	A	T	94	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYC2_RHOCB_001 *	L	108	T	CYC2_RHOCB	---	---	B	L	87	T
2	UniProt	VAR_CYC2_RHOCB_002 *	T	115	S	CYC2_RHOCB	---	---	B	T	94	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOCB	22-136	2	A:1-115 B:1-115

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOCB	22-136	1	A:1-115 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC2_RHOCB	22-136	1	- B:1-115

(no "Exon" information available for 1VYD)

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:116
 aligned with CYC2_RHOCB | P00094 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:116
                                    31        41        51        61        71        81        91       101       111       121       131      
           CYC2_RHOCB    22 GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPGAFLKEKLDDKKAKTGMAFKLAKGGEDVAAYLASVVK 137
               SCOP domains d1vyda_ A: Cytochrome c2                                                                                             SCOP domains
               CATH domains 1vydA00 A:1-116 Cytochrome c                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....ee.....eee.........................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------T------S---------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-115 UniProt: 22-136                                                                                 - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyd A   1 GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPGAFLKEKLDDKKAKTEMAFKLAKGGEDVAAYLASVVK 116
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with CYC2_RHOCB | P00094 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:116
                                    31        41        51        61        71        81        91       101       111       121       131      
           CYC2_RHOCB    22 GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPGAFLKEKLDDKKAKTGMAFKLAKGGEDVAAYLASVVK 137
               SCOP domains d1vydb_ B: Cytochrome c2                                                                                             SCOP domains
               CATH domains 1vydB00 B:1-116 Cytochrome c                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....ee.....eee.........................hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------T------S---------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-115 UniProt: 22-136                                                                                 - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyd B   1 GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPGAFLKEKLDDKKAKTEMAFKLAKGGEDVAAYLASVVK 116
                                    10        20        30        40        50        60        70        80        90       100       110

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: Cytochrome c2 (21)

Rhodobacter capsulatus [TaxId: 1061] (3)

1a	d1vyda_	A:
1b	d1vydb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

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

Homologous Superfamily: Cytochrome c (279)

Rhodobacter capsulatus. Organism_taxid: 1061. (3)

1a	1vydA00	A:1-116
1b	1vydB00	B:1-116

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYC2_RHOCB | P00094)

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.

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	CYC2_RHOCB \| P00094	:	1c2n 1c2r

1c2n	CYTOCHROME C2, NMR, 20 STRUCTURES
1c2r	CYTOCHROME C2

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