1SC6

Crystal Structure of W139G D-3-Phosphoglycerate dehydrogenase complexed with NAD+

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1sc6a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1sc6a2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1sc6a3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1sc6b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1sc6b2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1sc6b3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1sc6c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1sc6c2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1sc6c3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1sc6d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1sc6d2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1sc6d3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	D-lactate/D-glycerate dehydrogenase-like	8001019	4000099	SCOP2 (2022-06-29)
A	SCOP2 Family	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	8001020	4000051	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ACT-like	8001021	3000006	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ACT-like	8001021	3000006	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ACT-like	8001021	3000006	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ACT-like	8001021	3000006	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)
A	ACT	e1sc6A1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
A	2-Hacid_dh_C	e1sc6A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
A	2-Hacid_dh	e1sc6A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
B	ACT	e1sc6B1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
B	2-Hacid_dh_C	e1sc6B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
B	2-Hacid_dh	e1sc6B3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
C	ACT	e1sc6C1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
C	2-Hacid_dh_C	e1sc6C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
C	2-Hacid_dh	e1sc6C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
D	ACT	e1sc6D1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
D	2-Hacid_dh_C	e1sc6D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
D	2-Hacid_dh	e1sc6D3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	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	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	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	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	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	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (2-Hacid_dh_C)	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389.	Domain
A, B, C, D	PF22629	AHAS-like ACT domain (AHAS-like_ACT)	AHAS-like ACT domain	This entry represents the ACT domain found at the N-terminal of acetohydroxyacid synthase isozyme III from Escherichia coli and similar sequences.	Domain
A, B, C, D	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (2-Hacid_dh)	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-3-phosphoglycerate dehydrogenase	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADH binding cation binding NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADH binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors 2-hydroxyglutarate dehydrogenase activity catalytic activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor phosphoglycerate dehydrogenase activity identical protein binding protein binding	serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050223	D-isomer specific 2-hydroxyacid dehydrogenase	Family
A, B, C, D	IPR045865	ACT-like domain	Homologous Superfamily
A, B, C, D	IPR002912	ACT domain	Domain
A, B, C, D	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
A, B, C, D	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B, C, D	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain	Domain

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.