1NBB - JenaLib

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Title :   N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'

Authors :   T. H. Tahirov, S. Misaki, T. E. Meyer, M. A. Cusanovich, Y. Higuchi, N. Yasuoka

Date :   18 Mar 96 (Deposition) - 17 Aug 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   T. H. Tahirov, S. Misaki, T. E. Meyer, M. A. Cusanovich, Y. Higuchi, N. Yasuoka
Concerted Movement Of Side Chains In The Haem Vicinity Observed On Ligand Binding In Cytochrome C' From Rhodobacter Capsulatus.
Nat. Struct. Biol. V. 3 459 1996
PubMed-ID: 8612077 | Reference-DOI: 10.1038/NSB0596-459
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C'
	Chains	:	A, B
	Organism Scientific	:	RHODOBACTER CAPSULATUS
	Organism Taxid	:	1061
	Other Details	:	N-BUTYLISOCYANIDE BOUND TO HEME IRON
	Strain	:	M110

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NBN	2	Ligand/Ion	N-BUTYL ISOCYANIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NBN	1	Ligand/Ion	N-BUTYL ISOCYANIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NBN	1	Ligand/Ion	N-BUTYL ISOCYANIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:10 , PHE A:14 , MET A:21 , THR A:68 , GLU A:69 , PHE A:81 , LYS A:84 , GLY A:85 , CYS A:118 , CYS A:121 , HIS A:122 , ARG A:126 , NBN A:131	BINDING SITE FOR RESIDUE HEM A 130
2	AC2	SOFTWARE	PHE A:14 , VAL A:51 , HEM A:130	BINDING SITE FOR RESIDUE NBN A 131
3	AC3	SOFTWARE	LYS A:4 , ARG B:10 , PHE B:14 , MET B:21 , THR B:68 , GLU B:69 , PHE B:81 , LYS B:84 , GLY B:85 , THR B:117 , CYS B:118 , CYS B:121 , HIS B:122 , TYR B:125 , ARG B:126 , GLU B:128 , NBN B:131 , HOH B:149 , HOH B:172	BINDING SITE FOR RESIDUE HEM B 130
4	AC4	SOFTWARE	PHE B:14 , VAL B:51 , HEM B:130	BINDING SITE FOR RESIDUE NBN B 131

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

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

Asymmetric Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYCP_RHOCA_001 *	K	19	G	CYCP_RHOCA	---	---	A/B	G	19	G
2	UniProt	VAR_CYCP_RHOCA_002 *	S	30	A	CYCP_RHOCA	---	---	A/B	A	30	A
3	UniProt	VAR_CYCP_RHOCA_003 *	A	38	V	CYCP_RHOCA	---	---	A/B	V	38	V
4	UniProt	VAR_CYCP_RHOCA_004 *	A	42	K	CYCP_RHOCA	---	---	A/B	K	42	K
5	UniProt	VAR_CYCP_RHOCA_005 *	T	76	A	CYCP_RHOCA	---	---	A/B	A	76	A
6	UniProt	VAR_CYCP_RHOCA_006 *	A	79	D	CYCP_RHOCA	---	---	A/B	D	79	D
7	UniProt	VAR_CYCP_RHOCA_007 *	N	89	H	CYCP_RHOCA	---	---	A/B	H	89	H
8	UniProt	VAR_CYCP_RHOCA_008 *	D	90	E	CYCP_RHOCA	---	---	A/B	E	90	E
	* ID not provided by source

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

Biological Unit 1 (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYCP_RHOCA_001 *	K	19	G	CYCP_RHOCA	---	---	A	G	19	G
2	UniProt	VAR_CYCP_RHOCA_002 *	S	30	A	CYCP_RHOCA	---	---	A	A	30	A
3	UniProt	VAR_CYCP_RHOCA_003 *	A	38	V	CYCP_RHOCA	---	---	A	V	38	V
4	UniProt	VAR_CYCP_RHOCA_004 *	A	42	K	CYCP_RHOCA	---	---	A	K	42	K
5	UniProt	VAR_CYCP_RHOCA_005 *	T	76	A	CYCP_RHOCA	---	---	A	A	76	A
6	UniProt	VAR_CYCP_RHOCA_006 *	A	79	D	CYCP_RHOCA	---	---	A	D	79	D
7	UniProt	VAR_CYCP_RHOCA_007 *	N	89	H	CYCP_RHOCA	---	---	A	H	89	H
8	UniProt	VAR_CYCP_RHOCA_008 *	D	90	E	CYCP_RHOCA	---	---	A	E	90	E
	* ID not provided by source

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

Biological Unit 2 (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYCP_RHOCA_001 *	K	19	G	CYCP_RHOCA	---	---	B	G	19	G
2	UniProt	VAR_CYCP_RHOCA_002 *	S	30	A	CYCP_RHOCA	---	---	B	A	30	A
3	UniProt	VAR_CYCP_RHOCA_003 *	A	38	V	CYCP_RHOCA	---	---	B	V	38	V
4	UniProt	VAR_CYCP_RHOCA_004 *	A	42	K	CYCP_RHOCA	---	---	B	K	42	K
5	UniProt	VAR_CYCP_RHOCA_005 *	T	76	A	CYCP_RHOCA	---	---	B	A	76	A
6	UniProt	VAR_CYCP_RHOCA_006 *	A	79	D	CYCP_RHOCA	---	---	B	D	79	D
7	UniProt	VAR_CYCP_RHOCA_007 *	N	89	H	CYCP_RHOCA	---	---	B	H	89	H
8	UniProt	VAR_CYCP_RHOCA_008 *	D	90	E	CYCP_RHOCA	---	---	B	E	90	E
	* 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	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_RHOCA	5-127	2	A:5-127 B:5-127

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_RHOCA	5-127	1	A:5-127 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_RHOCA	5-127	1	- B:5-127

(no "Exon" information available for 1NBB)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:129
 aligned with CYCP_RHOCA | P00147 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           CYCP_RHOCA     1 ADTKEVLEAREAYFKSLGKSMKAMTGVAKSFDAEAAKAEAAALEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWTNMADFGAKGKAMNDAGAEVIAAANAGDATAFGAALQKLGGTCKACHDDYREED 129
               SCOP domains d1nbba_ A: Cytochrome c'                                                                                                          SCOP domains
               CATH domains 1nbbA00 A:1-129  [code=1.20.120.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........................hhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------G----------A-------V---K---------------------------------A--D---------HE--------------------------------------- SAPs(SNPs)
                    PROSITE ----CYTCII  PDB: A:5-127 UniProt: 5-127                                                                                        -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nbb A   1 ADTKEVLEAREAYFKSLGGSMKAMTGVAKAFDAEAAKVEAAKLEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWANMDDFGAKGKAMHEAGGAVIAAANAGDGAAFGAALQKLGGTCKACHDDYREED 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with CYCP_RHOCA | P00147 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           CYCP_RHOCA     1 ADTKEVLEAREAYFKSLGKSMKAMTGVAKSFDAEAAKAEAAALEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWTNMADFGAKGKAMNDAGAEVIAAANAGDATAFGAALQKLGGTCKACHDDYREED 129
               SCOP domains d1nbbb_ B: Cytochrome c'                                                                                                          SCOP domains
               CATH domains 1nbbB00 B:1-129  [code=1.20.120.10, no name defined]                                                                              CATH domains
           Pfam domains (1) ---Cytochrom_C_2-1nbbB01 B:4-126                                                                                              --- Pfam domains (1)
           Pfam domains (2) ---Cytochrom_C_2-1nbbB02 B:4-126                                                                                              --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........................hhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------G----------A-------V---K---------------------------------A--D---------HE--------------------------------------- SAPs(SNPs)
                    PROSITE ----CYTCII  PDB: B:5-127 UniProt: 5-127                                                                                        -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nbb B   1 ADTKEVLEAREAYFKSLGGSMKAMTGVAKAFDAEAAKVEAAKLEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWANMDDFGAKGKAMHEAGGAVIAAANAGDGAAFGAALQKLGGTCKACHDDYREED 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: Four-helical up-and-down bundle (308)

Superfamily: Cytochromes (82)

Family: Cytochrome c'-like (44)

Protein domain: Cytochrome c' (16)

Rhodobacter capsulatus [TaxId: 1061] (4)

1a	d1nbba_	A:
1b	d1nbbb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.10, no name defined] (45)

Rhodobacter capsulatus. Organism_taxid: 1061. Strain: m110 (2)

1a	1nbbA00	A:1-129
1b	1nbbB00	B:1-129

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cytochrom_C_2] (14)

Family: Cytochrom_C_2 (14)

Rhodobacter capsulatus (Rhodopseudomonas capsulata) (2)

1a	Cytochrom_C_2-1nbbB01	B:4-126
1b	Cytochrom_C_2-1nbbB02	B:4-126

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYCP_RHOCA | P00147)

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:0022900	electron transport chain	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: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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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