2CDQ | pdb_00002cdq

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine

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)
B	d2cdqb1	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	PyrH-like	Aspartokinase	MOUSE-EAR CRESS (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d2cdqb2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Aspartokinase allosteric domain-like	Aspartokinase	MOUSE-EAR CRESS (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d2cdqa1	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	PyrH-like	Aspartokinase	MOUSE-EAR CRESS (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d2cdqa2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Aspartokinase allosteric domain-like	Aspartokinase	MOUSE-EAR CRESS (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Carbamate kinase-like	8038705	3001310	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ACT-like	8038706	3000006	SCOP2B (2022-06-29)
A	SCOP2 Family	PyrH-like	8026326	4003224	SCOP2 (2022-06-29)
A	SCOP2 Family	Aspartokinase allosteric domain-like	8026327	4003690	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Carbamate kinase-like	8038705	3001310	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ACT-like	8038706	3000006	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	ACT_7_1	e2cdqB2	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_7_1	ECOD (1.6)
B	ACT_2	e2cdqB1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_2	ECOD (1.6)
B	AA_kinase	e2cdqB3	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: AA_kinase	ECOD (1.6)
A	ACT_7_1	e2cdqA2	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_7_1	ECOD (1.6)
A	ACT_2	e2cdqA1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT_2	ECOD (1.6)
A	AA_kinase	e2cdqA3	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: AA_kinase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
B	1.20.120.1320	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Aspartokinase, catalytic domain	CATH (4.3.0)
B	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
A	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
A	1.20.120.1320	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Aspartokinase, catalytic domain	CATH (4.3.0)
A	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	PF00696	Amino acid kinase family (AA_kinase)	Amino acid kinase family	-	Family
A, B	PF22468	ACT domain (ACT_9)	ACT domain	This entry represents the ACT domain, which is found twice in Aspartate kinase from Methanocaldococcus jannaschii, the enzyme that catalyses the phosphorylation of aspartic acid [6]. This domain folds as a four-stranded antiparallel sheet with two al ...	This entry represents the ACT domain, which is found twice in Aspartate kinase from Methanocaldococcus jannaschii, the enzyme that catalyses the phosphorylation of aspartic acid [6]. This domain folds as a four-stranded antiparallel sheet with two alpha-helices parallel to the sheet and located on one side of the sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ASPARTOKINASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding amino acid kinase activity kinase activity aspartate kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process threonine biosynthetic process threonine metabolic process	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001048	Aspartate/glutamate/uridylate kinase	Domain
A, B	IPR045865	ACT-like domain	Homologous Superfamily
A, B	IPR002912	ACT domain	Domain
A, B	IPR018042	Aspartate kinase, conserved site	Conserved Site
A, B	IPR047896	Aspartokinase 1, ACT domain 1	Domain
A, B	IPR041746	Lysine-sensitive aspartokinase catalytic domain	Domain
A, B	IPR042199	Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain	Homologous Superfamily
A, B	IPR054352	Aspartokinase, ACT domain	Domain
A, B	IPR001341	Aspartate kinase	Family
A, B	IPR047895	Aspartokinase 1, ACT domain 2	Domain
A, B	IPR036393	Acetylglutamate kinase-like 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 R01GM157729.