2GC7 | pdb_00002gc7

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2gc7a_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
E	d2gc7e_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
I	d2gc7i_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
M	d2gc7m_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d2gc7b_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
F	d2gc7f_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
J	d2gc7j_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
N	d2gc7n_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C	d2gc7c_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
G	d2gc7g_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
K	d2gc7k_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
O	d2gc7o_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D	d2gc7d_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c551	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
H	d2gc7h_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c551	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
L	d2gc7l_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c551	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
P	d2gc7p_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c551	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
B	SCOP2 Family	Methylamine dehydrogenase, L chain	8029442	4003481	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
D	SCOP2 Family	Monodomain cytochrome c	8029444	4000635	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Cytochrome c	8041823	3000815	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Cytochrome c	8041823	3000815	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Cytochrome c	8041823	3000815	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Cytochrome c	8041823	3000815	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Me-amine-dh_H	e2gc7A1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
E	Me-amine-dh_H	e2gc7E1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
I	Me-amine-dh_H	e2gc7I1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
M	Me-amine-dh_H	e2gc7M1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
B	Me-amine-dh_L	e2gc7B1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)
F	Me-amine-dh_L	e2gc7F1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)
J	Me-amine-dh_L	e2gc7J1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)
N	Me-amine-dh_L	e2gc7N1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)
C	Copper-bind	e2gc7C1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
G	Copper-bind	e2gc7G1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
K	Copper-bind	e2gc7K1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
O	Copper-bind	e2gc7O1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
D	Cytochrome_CBB3	e2gc7D1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
H	Cytochrome_CBB3	e2gc7H1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
L	Cytochrome_CBB3	e2gc7L1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
P	Cytochrome_CBB3	e2gc7P1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.2.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.2.0)
I	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.2.0)
M	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.2.0)
B	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.2.0)
F	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.2.0)
J	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.2.0)
N	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.2.0)
C	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.2.0)
G	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.2.0)
K	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.2.0)
O	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.2.0)
D	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.2.0)
H	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.2.0)
L	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.2.0)
P	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E, I, M	Methylamine dehydrogenase heavy chain	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity methylamine dehydrogenase (amicyanin) activity oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor catalytic activity aliphatic amine dehydrogenase activity	amine metabolic process methylamine metabolic process metabolic process cellular process	cellular anatomical structure periplasmic space
B, F, J, N	Methylamine dehydrogenase light chain	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity methylamine dehydrogenase (amicyanin) activity oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor catalytic activity aliphatic amine dehydrogenase activity	amine metabolic process metabolic process cellular process	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
C, G, K, O	Amicyanin	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding electron transfer activity	-	cellular anatomical structure periplasmic space
D, H, L, P	Cytochrome c-L	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	alcohol metabolic process small molecule metabolic process metabolic process cellular process methanol metabolic process primary alcohol metabolic process	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E, I, M	IPR009451	Amine dehydrogenase heavy chain	Family
A, E, I, M	IPR011044	Quinoprotein amine dehydrogenase, beta chain-like	Homologous Superfamily
A, E, I, M	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, E, I, M	IPR013476	Methylamine dehydrogenase heavy chain	Family
B, F, J, N	IPR004229	Methylamine dehydrogenase light chain	Family
B, F, J, N	IPR016008	Amine dehydrogenase light chain	Family
B, F, J, N	IPR036560	Methylamine/Aralkylamine dehydrogenase light chain superfamily	Homologous Superfamily
B, F, J, N	IPR013504	Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain	Domain
C, G, K, O	IPR035668	Amicyanin	Family
C, G, K, O	IPR052721	Electron Transfer Amicyanin	Family
C, G, K, O	IPR002386	Amicyanin/Pseudoazurin	Family
C, G, K, O	IPR013475	Amicyanin, Paracoccus/Methylobacterium	Family
C, G, K, O	IPR000923	Blue (type 1) copper domain	Domain
C, G, K, O	IPR028871	Blue (type 1) copper protein, binding site	Binding Site
C, G, K, O	IPR008972	Cupredoxin	Homologous Superfamily
C, G, K, O	IPR001235	Blue (type 1) copper protein, plastocyanin-type	Family
D, H, L, P	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
D, H, L, P	IPR009056	Cytochrome c-like domain	Domain
D, H, L, P	IPR009153	Cytochrome cL	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, F, J, N	TRQ	Parent Component: TRP RESID: AA0148 PSI-MOD : oxidation of tryptophan to L-tryptophyl quinone MOD:00157

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.