2J56

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2j56a_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d2j56b_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C [auth H]	d2j56h_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D [auth J]	d2j56j_	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 [auth L]	d2j56l_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
F [auth M]	d2j56m_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	automated matches	(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	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	Methylamine dehydrogenase L chain	8041821	3000932	SCOP2B (2022-06-29)
F [auth M]	SCOP2B Superfamily	Methylamine dehydrogenase L chain	8041821	3000932	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	Copper-bind	e2j56A1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
B	Copper-bind	e2j56B1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
C [auth H]	Me-amine-dh_H	e2j56H1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
D [auth J]	Me-amine-dh_H	e2j56J1	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 [auth L]	Me-amine-dh_L	e2j56L1	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 [auth M]	Me-amine-dh_L	e2j56M1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
C [auth H]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D [auth J]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E [auth L]	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.3.0)
F [auth M]	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00127	Copper binding proteins, plastocyanin/azurin family (Copper-bind)	Copper binding proteins, plastocyanin/azurin family	-	Domain
C [auth H], D [auth J]	PF06433	Methylamine dehydrogenase heavy chain (MADH) (Me-amine-dh_H)	Methylamine dehydrogenase heavy chain (MADH)	-	Repeat
E [auth L], F [auth M]	PF02975	Methylamine dehydrogenase, L chain (Me-amine-dh_L)	Methylamine dehydrogenase, L chain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	AMICYANIN	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding electron transfer activity	-	periplasmic space cellular anatomical entity
C [auth H], D [auth J]	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 amine dehydrogenase activity	amine metabolic process methylamine metabolic process organonitrogen compound metabolic process organic substance metabolic process metabolic process primary amino compound metabolic process	periplasmic space cellular anatomical entity
E [auth L], F [auth M]	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 amine dehydrogenase activity	amine metabolic process organonitrogen compound metabolic process organic substance metabolic process metabolic process	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035668	Amicyanin	Family
A, B	IPR002386	Amicyanin/Pseudoazurin	Family
A, B	IPR013475	Amicyanin, Paracoccus/Methylobacterium	Family
A, B	IPR000923	Blue (type 1) copper domain	Domain
A, B	IPR028871	Blue (type 1) copper protein, binding site	Binding Site
A, B	IPR008972	Cupredoxin	Homologous Superfamily
A, B	IPR001235	Blue (type 1) copper protein, plastocyanin-type	Family
C [auth H], D [auth J]	IPR009451	Amine dehydrogenase heavy chain	Family
C [auth H], D [auth J]	IPR011044	Quinoprotein amine dehydrogenase, beta chain-like	Homologous Superfamily
C [auth H], D [auth J]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth H], D [auth J]	IPR013476	Methylamine dehydrogenase heavy chain	Family
E [auth L], F [auth M]	IPR004229	Methylamine dehydrogenase light chain	Family
E [auth L], F [auth M]	IPR016008	Amine dehydrogenase light chain	Family
E [auth L], F [auth M]	IPR036560	Methylamine/Aralkylamine dehydrogenase light chain superfamily	Homologous Superfamily
E [auth L], F [auth M]	IPR013504	Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.