4OHF | pdb_00004ohf

Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with GMP from Legionella pneumophila, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1

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)
D	d4ohfd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5' nucleotidase-like	Cytosolic IMP-GMP specific 5'-nucleotidase	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)
C	d4ohfc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5' nucleotidase-like	Cytosolic IMP-GMP specific 5'-nucleotidase	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)
B	d4ohfb1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5' nucleotidase-like	Cytosolic IMP-GMP specific 5'-nucleotidase	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)
B	d4ohfb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)
A	d4ohfa1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5' nucleotidase-like	Cytosolic IMP-GMP specific 5'-nucleotidase	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)
A	d4ohfa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Legionella pneumophila subsp. pneumophila str. Philadelphia 1 ) [TaxId: 272624 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	HAD-like	8037871	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8037871	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8037871	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8037871	3001890	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)
D	5_nucleotid	e4ohfD1	A: alpha bundles	X: HAD superfamily helical bundle insertion domain	H: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase (From Topology)	T: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase	F: 5_nucleotid	ECOD (1.6)
D	5_nucleotid	e4ohfD2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: 5_nucleotid	ECOD (1.6)
C	5_nucleotid	e4ohfC2	A: alpha bundles	X: HAD superfamily helical bundle insertion domain	H: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase (From Topology)	T: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase	F: 5_nucleotid	ECOD (1.6)
C	5_nucleotid	e4ohfC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: 5_nucleotid	ECOD (1.6)
B	5_nucleotid	e4ohfB1	A: alpha bundles	X: HAD superfamily helical bundle insertion domain	H: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase (From Topology)	T: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase	F: 5_nucleotid	ECOD (1.6)
B	5_nucleotid	e4ohfB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: 5_nucleotid	ECOD (1.6)
A	5_nucleotid	e4ohfA2	A: alpha bundles	X: HAD superfamily helical bundle insertion domain	H: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase (From Topology)	T: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase	F: 5_nucleotid	ECOD (1.6)
A	5_nucleotid	e4ohfA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: 5_nucleotid	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D	1.20.58.1160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	1.20.58.1160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	1.20.58.1160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	1.20.58.1160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05761	5' nucleotidase family (5_nucleotid)	5' nucleotidase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytosolic IMP-GMP specific 5'-nucleotidase	phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity 5'-nucleotidase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D	IPR008380	HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase	Family
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR016695	Purine 5'-nucleotidase	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.