1U6K | pdb_00001u6k

TLS refinement of the structure of Se-methionine labelled Coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) from Methanopyrus kandleri

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	d1u6ka_	Alpha and beta proteins (a/b)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)
C	d1u6kc_	Alpha and beta proteins (a/b)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)
B	d1u6kb_	Alpha and beta proteins (a/b)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	8020474	4001041	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	8032854	3000556	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	8032854	3000556	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	8032854	3000556	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	MTD	e1u6kA1	A: alpha bundles	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	F: MTD	ECOD (develop294)
C	Pribosyltran	e1u6kC1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
B	Pribosyltran	e1u6kB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10830	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	CATH (4.3.0)
A	6.10.140.120	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.40.50.10830	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	CATH (4.3.0)
C	6.10.140.120	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	3.40.50.10830	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)	CATH (4.3.0)
B	6.10.140.120	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01993	methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase (MTD)	methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	F420-dependent methylenetetrahydromethanopterin dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity oxidoreductase activity, acting on the CH-NH group of donors methylenetetrahydromethanopterin dehydrogenase activity	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process methanogenesis, from carbon dioxide anaerobic respiration cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process methanogenesis, from carbon dioxide anaerobic respiration small molecule metabolic process one-carbon metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR036080	F420-dependent methylenetetrahydromethanopterin dehydrogenase superfamily	Homologous Superfamily
A, B, C	IPR002844	F420-dependent methylenetetrahydromethanopterin dehydrogenase	Family

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.