2VHW

Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the open and closed conformation

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)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8065358	3000044	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	AlaDh_PNT_C	e2vhwA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
A	AlaDh_PNT_N	e2vhwA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	ECOD (1.6)
B	AlaDh_PNT_C	e2vhwB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
B	AlaDh_PNT_N	e2vhwB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	ECOD (1.6)
C	AlaDh_PNT_C	e2vhwC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
C	AlaDh_PNT_N	e2vhwC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	ECOD (1.6)
D	AlaDh_PNT_C	e2vhwD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
D	AlaDh_PNT_N	e2vhwD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	ECOD (1.6)
E	AlaDh_PNT_C	e2vhwE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
E	AlaDh_PNT_N	e2vhwE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	ECOD (1.6)
F	AlaDh_PNT_C	e2vhwF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AlaDh_PNT_C	ECOD (1.6)
F	AlaDh_PNT_N	e2vhwF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AlaDh_PNT_N	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)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like 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)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	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)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like 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	PF05222	Alanine dehydrogenase/PNT, N-terminal domain (AlaDh_PNT_N)	Alanine dehydrogenase/PNT, N-terminal domain	This family now also contains the lysine 2-oxoglutarate reductases.	Domain
A, B, C, D, E A, B, C, D, E, F	PF01262	Alanine dehydrogenase/PNT, C-terminal domain (AlaDh_PNT_C)	Alanine dehydrogenase/PNT, C-terminal domain	This family now also contains the lysine 2-oxoglutarate reductases.	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	ALANINE DEHYDROGENASE	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors alanine dehydrogenase activity oxidoreductase activity catalytic activity cation binding ion binding metal ion binding	response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process alanine catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process alanine catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process pyruvate family amino acid catabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process L-alanine catabolic process cellular metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process L-alanine metabolic process small molecule catabolic process alanine metabolic process	extracellular region cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR007886	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008142	Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008141	Alanine dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR008143	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR007698	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-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.