2XF8 | pdb_00002xf8

Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD cofactor analog (3-Chloroacetyl adenine pyridine dinucleotide) and sulfate anion

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAPDH-like	8068929	3000043	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P	e2xf8P3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Peptidase_M49	F:	ECOD (20:10:01)
O	e2xf8O1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
N	e2xf8N1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
M	e2xf8M1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
L	e2xf8L1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: RNA_pol_Rpb2_4	F:	ECOD (20:10:01)
K	e2xf8K1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
J	e2xf8J1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
I	e2xf8I1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
H	e2xf8H3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Peptidase_M49	F:	ECOD (20:10:01)
G	e2xf8G1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
F	e2xf8F1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
E	e2xf8E1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
D	e2xf8D3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Peptidase_M49	F:	ECOD (20:10:01)
C	e2xf8C1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
B	e2xf8B1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)
A	e2xf8A1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: YjeF_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
P	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
O	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
O	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
N	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
N	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
M	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
M	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
L	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
L	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
K	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
K	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
J	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
J	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
I	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
I	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain (Gp_dh_C)	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain (Gp_dh_N)	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.	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	D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE	oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors erythrose-4-phosphate dehydrogenase activity catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors erythrose-4-phosphate dehydrogenase activity catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process pyridoxine biosynthetic process pyridoxine metabolic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process primary metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036291	NAD(P)-binding 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	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR006422	D-erythrose-4-phosphate dehydrogenase	Family