3DFY | pdb_00003dfy

Crystal structure of apo dipeptide epimerase from Thermotoga maritima

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	d3dfya2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d3dfya1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d3dfyb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d3dfyb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d3dfyc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d3dfyc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d3dfyd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d3dfyd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d3dfye2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d3dfye1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d3dfyf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d3dfyf1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
G	d3dfyg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
G	d3dfyg1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
H	d3dfyh2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
H	d3dfyh1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
I	d3dfyi2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
I	d3dfyi1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
J	d3dfyj2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
J	d3dfyj1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
K	d3dfyk2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
K	d3dfyk1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
L	d3dfyl2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
L	d3dfyl1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
M	d3dfym2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
M	d3dfym1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
N	d3dfyn2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
N	d3dfyn1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
O	d3dfyo2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
O	d3dfyo1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
P	d3dfyp2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
P	d3dfyp1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	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	zf-CCCH_4	e3dfyA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
B	zf-CCCH_4	e3dfyB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
C	zf-CCCH_4	e3dfyC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
D	zf-CCCH_4	e3dfyD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
E	zf-CCCH_4	e3dfyE1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
F	zf-CCCH_4	e3dfyF1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
G	zf-CCCH_4	e3dfyG1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
H	zf-CCCH_4	e3dfyH1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
I	zf-CCCH_4	e3dfyI1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
J	zf-CCCH_4	e3dfyJ1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
K	zf-CCCH_4	e3dfyK1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
L	zf-CCCH_4	e3dfyL1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
M	zf-CCCH_4	e3dfyM1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
N	zf-CCCH_4	e3dfyN1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
O	zf-CCCH_4	e3dfyO1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
P	zf-CCCH_4	e3dfyP1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)

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)
J	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
J	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
K	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
K	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
L	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
L	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
M	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
M	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
N	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
N	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
O	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
O	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
P	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
P	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, J, K, L, M, N, O, P	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, J, K, L, M, N, O, P	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, J, K, L, M, N, O, P	Muconate cycloisomerase	isomerase activity racemase and epimerase activity L-Ala-D/L-Glu epimerase activity racemase and epimerase activity, acting on amino acids and derivatives catalytic activity cation binding ion binding binding metal ion binding small molecule binding	metabolic process cellular process peptide metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization catabolic process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule 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, J, K, L, M, N, O, P	IPR029065	Enolase_C-like	Unknown
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR034603	Dipeptide epimerase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR013341	Mandelate racemase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR053602	Mandelate racemase/muconate lactonizing enzyme-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR029017	Enolase-like, N-terminal	Homologous Superfamily