1PBY | pdb_00001pby

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1pbyc_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Quinohemoprotein amine dehydrogenase C chain	Quinohemoprotein amine dehydrogenase C chain	Quinohemoprotein amine dehydrogenase C chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1pbyb_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	Quinohemoprotein amine dehydrogenase B chain	Quinohemoprotein amine dehydrogenase B chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
A	d1pbya1	All alpha proteins	Cytochrome c	Cytochrome c	Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2	Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
A	d1pbya3	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5	Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
A	d1pbya5	All beta proteins	Streptavidin-like	Quinohemoprotein amine dehydrogenase A chain, domain 3	Quinohemoprotein amine dehydrogenase A chain, domain 3	Quinohemoprotein amine dehydrogenase A chain, domain 3	(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)
C	SCOP2 Family	Guinohemoprotein amine dehydrogenase C chain	8026102	4002937	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Quinohemoprotein amine dehydrogenase C chain	8038481	3001924	SCOP2 (2022-06-29)
B	SCOP2 Family	Quinohemoprotein amine dehydrogenase B chain	8026100	4003131	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8038479	3001671	SCOP2 (2022-06-29)
A	SCOP2 Family	Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2	8026097	4002862	SCOP2 (2022-06-29)
A	SCOP2 Family	Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2	8026098	4002862	SCOP2 (2022-06-29)
A	SCOP2 Family	Quinohemoprotein amine dehydrogenase A chain, domain 3	8026099	4003130	SCOP2 (2022-06-29)
A	SCOP2 Family	Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5	8055062	4007525	SCOP2 (2022-06-29)
A	SCOP2 Family	Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5	8055408	4007525	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c	8038476	3000815	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c	8038477	3000815	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Quinohemoprotein amine dehydrogenase A chain, domain 3	8038478	3000299	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8055063	3000070	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8055409	3000070	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	QH-AmDH_gamma	e1pbyC1	A: alpha arrays	X: Quinohemoprotein amine dehydrogenase C chain (From Topology)	H: Quinohemoprotein amine dehydrogenase C chain (From Topology)	T: Quinohemoprotein amine dehydrogenase C chain	F: QH-AmDH_gamma	ECOD (1.6)
B	Lactonase_2	e1pbyB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Lactonase_2	ECOD (1.6)
A	Qn_am_d_aII	e1pbyA1	A: beta barrels	X: Lipocalins/Streptavidin	H: Quinohemoprotein amine dehydrogenase A chain, domain 3-like (From Topology)	T: Quinohemoprotein amine dehydrogenase A chain, domain 3-like	F: Qn_am_d_aII	ECOD (1.6)
A	Qn_am_d_aIII	e1pbyA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Qn_am_d_aIII	ECOD (1.6)
A	Qn_am_d_aIV	e1pbyA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Qn_am_d_aIV	ECOD (1.6)
A	Dehyd-heme_bind	e1pbyA4	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Dehyd-heme_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	4.10.940.10	Few Secondary Structures	Irregular	Quinohemoprotein amine dehydrogenase	Quinohemoprotein amine dehydrogenase, gamma subunit structural domain	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.40.128.120	Mainly Beta	Beta Barrel	Lipocalin	Quinohemoprotein amine dehydrogenase alpha subunit, domain 2	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	quinohemoprotein amine dehydrogenase 9 kDa subunit	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity catalytic activity	-	cellular anatomical structure periplasmic space
B	quinohemoprotein amine dehydrogenase 40 kDa subunit	-	-	-
A	quinohemoprotein amine dehydrogenase 60 kDa subunit	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036487	Quinohemoprotein amine dehydrogenase, gamma subunit structural domain superfamily	Homologous Superfamily
C	IPR047830	Quinohemoprotein amine dehydrogenase subunit gamma	Family
C	IPR015084	Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain	Domain
B	IPR023879	Quinohemoprotein amine dehydrogenase, beta subunit	Family
B	IPR011044	Quinoprotein amine dehydrogenase, beta chain-like	Homologous Superfamily
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR051200	Multi-functional host-pathogen interaction and enzymatic activity protein	Family
A	IPR015183	Quinohemoprotein amine dehydrogenase, alpha subunit domain III	Domain
A	IPR015182	Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain	Domain
A	IPR036718	Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 superfamily	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR015184	Quinohemoprotein amine dehydrogenase, alpha subunit domain IV	Domain
A	IPR023887	Quinohemoprotein amine dehydrogenase, alpha subunit	Family
A	IPR009111	Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2	Domain

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.