4MCJ | pdb_00004mcj

Crystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
C	SCOP2 Family	BDI_0649-like	8044703	4004089	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8052029	3001392	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)
J	WD40, Beta-prop_NOL10_N	e4mcjJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
I	WD40, Beta-prop_NOL10_N	e4mcjI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
H	WD40, Beta-prop_NOL10_N	e4mcjH1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
G	WD40, Beta-prop_NOL10_N	e4mcjG1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
F	WD40, Beta-prop_NOL10_N	e4mcjF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
E	WD40, Beta-prop_NOL10_N	e4mcjE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
D	WD40, Beta-prop_NOL10_N	e4mcjD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
C	WD40, Beta-prop_NOL10_N	e4mcjC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
B	WD40, Beta-prop_NOL10_N	e4mcjB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: WD40, Beta-prop_NOL10_N	ECOD (v294.1)
A	ABC_membrane	e4mcjA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Hairpin loop containing domain-like	T: ACT-like	F: ABC_membrane	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
J	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
I	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
H	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
G	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
F	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
E	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
D	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
C	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
B	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (4.3.0)
A	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	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, I, J	PF15891	Nucleoside 2-deoxyribosyltransferase like (Nuc_deoxyri_tr2)	Nucleoside 2-deoxyribosyltransferase like	-	Family

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR039470	Nucleoside 2-deoxyribosyltransferase-like	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.

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