Annotations: 3VPB

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RimK	e3vpbA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
A	LysX_arch	e3vpbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
B	RimK	e3vpbB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
B	LysX_arch	e3vpbB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
C	RimK	e3vpbC1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
C	LysX_arch	e3vpbC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
D	RimK	e3vpbD1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: RimK	ECOD (1.6)
D	LysX_arch	e3vpbD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: LysX_arch	ECOD (1.6)
E	TF_Zn_Ribbon_1	e3vpbE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TF_Zn_Ribbon_1	ECOD (1.6)
F	TF_Zn_Ribbon_1	e3vpbF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TF_Zn_Ribbon_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
E	2.20.28.160	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
F	2.20.28.160	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08443	RimK-like ATP-grasp domain (RimK)	RimK-like ATP-grasp domain	This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK [1].	Domain
A, B, C, D	PF22626	LysX preATP-grasp domain (LysX_preATP_grasp)	LysX preATP-grasp domain	This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX, ArgX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxy ...	This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX, ArgX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW [1,2]. ArgX catalyses the ATP-dependent formation of a covalent bond between the amino group of glutamate and the gamma-carboxyl group of the C-terminal glutamate residue in LysW [2].	Domain
E, F	PF21344	Alpha-aminoadipate carrier protein LysW-like, globular domain (Zn_ribbon_LysW)	Alpha-aminoadipate carrier protein LysW-like, globular domain	This domain is found in a group of prokaryotic proteins, including Alpha-aminoadipate carrier protein LysW from Thermus thermophilus. LysW is an amino group-carrier protein that plays an important role in lysine biosynthesis. This globular domain is ...	This domain is found in a group of prokaryotic proteins, including Alpha-aminoadipate carrier protein LysW from Thermus thermophilus. LysW is an amino group-carrier protein that plays an important role in lysine biosynthesis. This globular domain is composed of five beta-strands and adopts a similar structure to members of the zinc ribbon superfamily. It is responsible for the binding of a zinc atom [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative acetylornithine deacetylase	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 acid-amino acid ligase activity coenzyme F420-2 alpha-glutamyl ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion binding identical protein binding protein binding	lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic 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 lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic 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 primary metabolic 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 alpha-amino acid biosynthetic process L-arginine biosynthetic process glutamine family amino acid biosynthetic process glutamine family amino acid metabolic process arginine metabolic process macromolecule modification protein metabolic process macromolecule metabolic process protein modification process	cellular anatomical structure intracellular anatomical structure cytoplasm
E, F	Alpha-aminoadipate carrier protein lysW	cation binding ion binding binding metal ion binding small molecule binding	L-arginine biosynthetic process oxoacid metabolic process glutamine family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process arginine metabolic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-arginine biosynthetic process oxoacid metabolic process glutamine family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process arginine metabolic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid 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 alpha-amino acid biosynthetic process lysine metabolic process lysine biosynthetic process via aminoadipic acid aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process lysine biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011761	ATP-grasp fold	Domain
A, B, C, D	IPR011870	Lysine biosynthesis enzyme LysX	Family
A, B, C, D	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C, D	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B, C, D	IPR004666	Ribosomal bS6 modification enzyme RimK/Lysine biosynthesis enzyme LysX	Family
A, B, C, D	IPR054562	LysX/ArgX, preATP-grasp domain	Domain
A, B, C, D	IPR013651	ATP-grasp fold, RimK-type	Domain
E, F	IPR005906	Lysine biosynthesis protein LysW	Family

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.