1CYC - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION

Authors :   N. Tanaka, T. Yamane, T. Tsukihara, T. Ashida, M. Kakudo

Date :   01 Aug 76 (Deposition) - 06 Oct 76 (Release) - 24 Feb 09 (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 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tanaka, T. Yamane, T. Tsukihara, T. Ashida, M. Kakudo
The Crystal Structure Of Bonito (Katsuo) Ferrocytochrome C At 2. 3 A Resolution. Ii. Structure And Function.
J. Biochem. (Tokyo) V. 77 147 1975
PubMed-ID: 166072
(for further references see the PDB file header)

Molecule 1 - FERROCYTOCHROME C
	Chains	:	A, B
	Engineered	:	YES
	Organism Common	:	SKIPJACK TUNA
	Organism Scientific	:	KATSUWONUS PELAMIS
	Organism Taxid	:	8226

		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:13 , CYS A:14 , CYS A:17 , HIS A:18 , LEU A:32 , LEU A:35 , ARG A:38 , THR A:40 , TYR A:46 , TYR A:48 , ASN A:52 , TRP A:59 , THR A:78 , LYS A:79 , MET A:80 , PHE A:82 , HOH A:105	BINDING SITE FOR RESIDUE HEM A 104
2	AC2	SOFTWARE	LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , LEU B:32 , LEU B:35 , ARG B:38 , THR B:40 , TYR B:46 , TYR B:48 , ASN B:52 , TRP B:59 , THR B:78 , LYS B:79 , MET B:80 , PHE B:82	BINDING SITE FOR RESIDUE HEM B 104

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_KATPE	2-103	2	A:1-102 B:1-102

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_KATPE	2-103	1	A:1-102 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_KATPE	2-103	1	- B:1-102

(no "Exon" information available for 1CYC)

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
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Chain A from PDB  Type:PROTEIN  Length:103
 aligned with CYC_KATPE | P00025 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
            CYC_KATPE     2 GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 104
               SCOP domains d1cyca_ A: Mitochondrial cytochrome c                                                                   SCOP domains
               CATH domains 1cycA00 A:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhh...............................hhhhhhh....hhhhhhhhhh....................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-102 UniProt: 2-103                                                                     - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1cyc A   1 GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with CYC_KATPE | P00025 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
            CYC_KATPE     2 GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 104
               SCOP domains d1cycb_ B: Mitochondrial cytochrome c                                                                   SCOP domains
               CATH domains 1cycB00 B:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhh...............................hhhhhhh....hhhhhhhhhh....................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 2-103                                                                     - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1cyc B   1 GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
                                    10        20        30        40        50        60        70        80        90       100

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(

)

Folds(

)

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: Mitochondrial cytochrome c (81)

Bonito (Katsuwonus pelamis) [TaxId: 8226] (1)

1a	d1cyca_	A:
1b	d1cycb_	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)

Skipjack tuna (Katsuwonus pelamis) (1)

1a	1cycA00	A:1-103
1b	1cycB00	B:1-103

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYC_KATPE | P00025)

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.
cellular component
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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