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
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)
F [auth B]	d1mdab_	All beta proteins	Cupredoxin-like	Cupredoxins	Plastocyanin/azurin-like	Amicyanin	(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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	Cupredoxins	8035199	3000886	SCOP2B (2022-06-29)
E [auth A]	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)
F [auth B]	Copper-bind	e1mdaB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
E [auth A]	Copper-bind	e1mdaA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D [auth M]	CBM_10	e1mdaM1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: Type X cellulose binding domain, CBDX	T: Type X cellulose binding domain, CBDX	F: CBM_10	ECOD (v294.1)
B [auth L]	CBM_10	e1mdaL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: Type X cellulose binding domain, CBDX	T: Type X cellulose binding domain, CBDX	F: CBM_10	ECOD (v294.1)
C [auth J]	DPPIV_N	e1mdaJ1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DPPIV_N	ECOD (v294.1)
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 (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.