Annotations: 3KJK

Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
I	d3kjki_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
L	d3kjkl_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
K	d3kjkk_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
J	d3kjkj_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
H	d3kjkh_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
G	d3kjkg_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
F	d3kjkf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
E	d3kjke_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
D	d3kjkd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
C	d3kjkc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
B	d3kjkb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
A	d3kjka_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YjgF-like	8059851	3001733	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)
I	Glyco_hydro_30	e3kjkI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
L	Glyco_hydro_30	e3kjkL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
K	Glyco_hydro_30	e3kjkK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
J	Glyco_hydro_30	e3kjkJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
H	Glyco_hydro_30	e3kjkH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
G	Glyco_hydro_30	e3kjkG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
F	Glyco_hydro_30	e3kjkF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
E	Glyco_hydro_30	e3kjkE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
D	Glyco_hydro_30	e3kjkD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
C	Glyco_hydro_30	e3kjkC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
B	Glyco_hydro_30	e3kjkB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)
A	Glyco_hydro_30	e3kjkA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Glyco_hydro_30	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
L	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
K	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
J	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
H	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
G	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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, K, L	PF01042	Endoribonuclease L-PSP (Ribonuc_L-PSP)	Endoribonuclease L-PSP	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. Yjg ...	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].	Domain

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, K, L	IPR019897	RidA, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035959	RutC-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035709	RutC family, YoaB-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006175	YjgF/YER057c/UK114 family	Family

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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.