1JC4 | pdb_00001jc4

Crystal Structure of Se-Met Methylmalonyl-CoA Epimerase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d1jc4d_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
C	d1jc4c_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
B	d1jc4b_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
A	d1jc4a_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
A	SCOP2 Family	Methylmalonyl-CoA epimerase	8021945	4003519	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	3-dmu-9_3-mt	e1jc4D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
C	3-dmu-9_3-mt	e1jc4C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
B	3-dmu-9_3-mt	e1jc4B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
A	Glyoxalase	e1jc4A1	A: a+b two layers	X: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	H: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	T: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	F: Glyoxalase	ECOD (develop294)
A	Glyoxalase_4	e1jc4A2	A: a+b two layers	X: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	H: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	T: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	F: Glyoxalase_4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
C	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
B	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
A	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Methylmalonyl-CoA epimerase	cation binding ion binding binding metal ion binding small molecule binding isomerase activity racemase and epimerase activity methylmalonyl-CoA epimerase activity catalytic activity	nucleoside phosphate metabolic process L-methylmalonyl-CoA metabolic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017515	Methylmalonyl-CoA epimerase	Family
A, B, C, D	IPR037523	Vicinal oxygen chelate (VOC), core domain	Domain
A, B, C, D	IPR051785	Methylmalonyl-CoA/ethylmalonyl-CoA epimerase	Family
A, B, C, D	IPR029068	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Homologous Superfamily

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.