4QNK | pdb_00004qnk

The structure of wt A. thaliana IGPD2 in complex with Mn2+ and phosphate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d4qnkh2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
H	d4qnkh1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
G	d4qnkg2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
G	d4qnkg1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d4qnkf2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d4qnkf1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d4qnke2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d4qnke1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d4qnkd2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d4qnkd1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4qnkc2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4qnkc1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4qnkb2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4qnkb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4qnka2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Imidazole glycerol phosphate dehydratase	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4qnka1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	GCD14	e4qnkH1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
G	GCD14	e4qnkG1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
F	GCD14	e4qnkF1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
E	GCD14	e4qnkE1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
D	GCD14	e4qnkD1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
C	GCD14	e4qnkC1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
B	GCD14	e4qnkB1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
A	GCD14	e4qnkA1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
G	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
F	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.230.40	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	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	PF00475	Imidazoleglycerol-phosphate dehydratase (IGPD)	Imidazoleglycerol-phosphate dehydratase	-	Family

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	Imidazoleglycerol-phosphate dehydratase 2, chloroplastic	imidazoleglycerol-phosphate dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding ion binding binding metal ion binding small molecule binding	oxoacid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process imidazole-containing compound metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process imidazole-containing compound metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process aromatic amino acid family biosynthetic process aromatic amino acid 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 L-histidine biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000807	Imidazoleglycerol-phosphate dehydratase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR038494	Imidazole glycerol phosphate dehydratase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020565	Imidazoleglycerol-phosphate dehydratase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020568	Ribosomal protein uS5 domain 2-type 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.