3Q4D

Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d3q4da2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
A	d3q4da1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
B	d3q4db2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
B	d3q4db1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
C	d3q4dc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
C	d3q4dc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
D	d3q4dd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
D	d3q4dd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
E	d3q4de2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
E	d3q4de1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
F	d3q4df2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
F	d3q4df1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
G	d3q4dg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
G	d3q4dg1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
H	d3q4dh2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
H	d3q4dh1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
I	d3q4di2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)
I	d3q4di1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Cytophaga hutchinsonii ATCC 33406 ) [TaxId: 269798 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF02746	e3q4dA1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
A	PF13378	e3q4dA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
B	PF02746	e3q4dB1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
B	PF13378	e3q4dB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
C	PF02746	e3q4dC1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
C	PF13378	e3q4dC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
D	PF02746	e3q4dD1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
D	PF13378	e3q4dD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
E	PF02746	e3q4dE1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
E	PF13378	e3q4dE2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
F	PF02746	e3q4dF1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
F	PF13378	e3q4dF2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
G	PF02746	e3q4dG1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
G	PF13378	e3q4dG2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
H	PF02746	e3q4dH1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
H	PF13378	e3q4dH2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
I	PF02746	e3q4dI1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
I	PF13378	e3q4dI2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
B	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
E	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
E	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
F	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
F	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
G	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
G	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
H	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
H	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
I	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
I	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	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	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain (MR_MLE_N)	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain	SCOP reports fold similarity with enolase N-terminal domain.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	PF13378	Enolase C-terminal domain-like (MR_MLE_C)	Enolase C-terminal domain-like	This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40.	Domain

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, I	Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isomerase activity racemase and epimerase activity catalytic activity racemase and epimerase activity, acting on amino acids and derivatives	organic substance metabolic process metabolic process peptide metabolic 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, I	IPR029065	Enolase C-terminal domain-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR034603	Dipeptide epimerase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR036849	Enolase-like, C-terminal domain superfamily	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 R01GM133198.