Annotations: 6VIM

P. putida mandelate racemase co-crystallized with phenylboronic acid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d6vimh2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
H	d6vimh1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
G	d6vimg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
G	d6vimg1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
F	d6vimf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
F	d6vimf1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
E	d6vime2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
E	d6vime1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d6vimd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d6vimd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d6vimc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d6vimc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d6vimb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d6vimb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d6vima2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d6vima1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase C-terminal domain-like	8043629	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase N-terminal domain-like	8035151	3001064	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	Ldh_1_C	e6vimH1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
G	Ldh_1_C	e6vimG1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
F	Ldh_1_C	e6vimF1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
E	Ldh_1_C	e6vimE1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
D	Ldh_1_C	e6vimD1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
C	Ldh_1_C	e6vimC1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
B	Ldh_1_C	e6vimB1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.2)
A		e6vimA1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.2)

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	Mandelate racemase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity racemase and epimerase activity, acting on hydroxy acids and derivatives isomerase activity mandelate racemase activity racemase and epimerase activity	carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process mandelate catabolic process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process amino acid metabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029065	Enolase_C-like	Unknown
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR046945	L-rhamnonate dehydratase-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013341	Mandelate racemase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015654	Mandelate racemase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029017	Enolase-like, N-terminal	Homologous Superfamily

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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.