1MDA | pdb_00001mda

CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND 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
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 [auth H]	d1mdah_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	Methylamine dehydrogenase, H-chain	Methylamine dehydrogenase, H-chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C [auth J]	d1mdaj_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	Methylamine dehydrogenase, H-chain	Methylamine dehydrogenase, H-chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B [auth L]	d1mdal_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D [auth M]	d1mdam_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
E [auth A]	d1mdaa_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
F [auth B]	d1mdab_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(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)
E [auth A]	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Cupredoxins	8035199	3000886	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 [auth H]	Me-amine-dh_H	e1mdaH1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
C [auth J]	Me-amine-dh_H	e1mdaJ1	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 [auth L]	Me-amine-dh_L	e1mdaL1	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)
D [auth M]	Me-amine-dh_L	e1mdaM1	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)
E [auth A]	Copper-bind	e1mdaA1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)
F [auth B]	Copper-bind	e1mdaB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: Copper-bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF00127	Copper binding proteins, plastocyanin/azurin family (Copper-bind)	Copper binding proteins, plastocyanin/azurin family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth J]	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)	-	-	-
B [auth L], D [auth M]	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)	-	-	-
E [auth A], F [auth B]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR035668	Amicyanin	Family
E [auth A], F [auth B]	IPR052721	Electron Transfer Amicyanin	Family
E [auth A], F [auth B]	IPR002386	Amicyanin/Pseudoazurin	Family
E [auth A], F [auth B]	IPR013475	Amicyanin, Paracoccus/Methylobacterium	Family
E [auth A], F [auth B]	IPR000923	Blue (type 1) copper domain	Domain
E [auth A], F [auth B]	IPR028871	Blue (type 1) copper protein, binding site	Binding Site
E [auth A], F [auth B]	IPR008972	Cupredoxin	Homologous Superfamily
E [auth A], F [auth B]	IPR001235	Blue (type 1) copper protein, plastocyanin-type	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth L], D [auth M]	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.