6ND3

wild-type choline TMA lyase in complex with betaine aldehyde

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)
C	d6nd3c_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
D	d6nd3d_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
E	d6nd3e_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
F	d6nd3f_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
G	d6nd3g_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
H	d6nd3h_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
A	d6nd3a_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)
B	d6nd3b_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	Desulfovibrio desulfuricans (strain G20) (Oleidesulfovibrio alaskensis G20 ) [TaxId: 207559 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	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)
C	PF02901	e6nd3C1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
C	PF01228	e6nd3C2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
D	PF02901	e6nd3D1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
D	PF01228	e6nd3D2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
E	PF02901	e6nd3E1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
E	PF01228	e6nd3E2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
F	PF02901	e6nd3F1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
F	PF01228	e6nd3F2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
G	PF02901	e6nd3G1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
G	PF01228	e6nd3G2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
H	PF02901	e6nd3H1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
H	PF01228	e6nd3H2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
A	PF02901	e6nd3A1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
A	PF01228	e6nd3A2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
B	PF02901	e6nd3B1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02901	ECOD (1.6)
B	PF01228	e6nd3B2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
D	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
E	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
F	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
G	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
H	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
A	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
B	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01228	Glycine radical (Gly_radical)	Glycine radical	-	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF02901	Pyruvate formate lyase-like (PFL-like)	Pyruvate formate lyase-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Choline trimethylamine-lyase	choline binding cation binding ion binding binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity lyase activity catalytic activity carbon-nitrogen lyase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process cellular biogenic amine catabolic process choline catabolic process ammonium ion metabolic process amine metabolic process organic substance metabolic process choline metabolic process metabolic process organic substance catabolic process amine catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004184	Pyruvate formate lyase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001150	Glycine radical domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019777	Formate C-acetyltransferase glycine radical, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR030897	Choline trimethylamine-lyase	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 R01GM133198.