6ND3 | pdb_00006nd3

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)
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	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)
F	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)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8087207	3001069	SCOP2B (2022-06-29)
C	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)
A	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)
H	DNA_gyraseB_C,Toprim	e6nd3H1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
G	DNA_gyraseB_C,Toprim	e6nd3G1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
F	DNA_gyraseB_C,Toprim	e6nd3F1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
E	DNA_gyraseB_C,Toprim	e6nd3E1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
D	DNA_gyraseB_C,Toprim	e6nd3D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
C	DNA_gyraseB_C,Toprim	e6nd3C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
B	DNA_gyraseB_C,Toprim	e6nd3B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
A	DNA_gyraseB_C,Toprim	e6nd3A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
F	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)
D	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
C	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)
A	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 choline trimethylamine lyase activity catalytic activity carbon-nitrogen lyase activity	amine metabolic process catabolic process choline metabolic process metabolic process cellular process choline catabolic process biogenic amine catabolic process amine catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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	IPR051215	Glycyl Radical Enzyme	Family
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.