8HCN | pdb_00008hcn

CryoEM Structure of Klebsiella pneumoniae UreD/urease complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	F_UNCLASSIFIED	e8hcnL1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Urease accessory protein ureH (From Topology)	T: Urease accessory protein ureH	F: F_UNCLASSIFIED	ECOD (1.6)
H	F_UNCLASSIFIED	e8hcnH1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Urease accessory protein ureH (From Topology)	T: Urease accessory protein ureH	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8hcnD1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Urease accessory protein ureH (From Topology)	T: Urease accessory protein ureH	F: F_UNCLASSIFIED	ECOD (1.6)
K	F_UNCLASSIFIED	e8hcnK1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
K	F_UNCLASSIFIED	e8hcnK2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8hcnG1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8hcnG2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hcnC2	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hcnC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: F_UNCLASSIFIED	ECOD (1.6)
J	F_UNCLASSIFIED	e8hcnJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8hcnF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8hcnB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: F_UNCLASSIFIED	ECOD (1.6)
I	F_UNCLASSIFIED	e8hcnI1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8hcnE1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8hcnA1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (utative)
K	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (utative)
G	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (utative)
G	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (utative)
C	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (utative)
C	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (utative)
I	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (utative)
E	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (utative)
A	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H, L	Urease accessory protein UreD	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm
C, G, K	Urease subunit alpha	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	nitrogen cycle metabolic process catabolic process small molecule metabolic process metabolic process cellular process urea catabolic process small molecule catabolic process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B, F, J	Urease subunit beta	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	nitrogen cycle metabolic process catabolic process small molecule metabolic process metabolic process cellular process urea catabolic process small molecule catabolic process urea metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm urease complex
A, E, I	Urease subunit gamma	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	nitrogen cycle metabolic process catabolic process small molecule metabolic process metabolic process cellular process urea catabolic process small molecule catabolic process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H, L	IPR002669	Urease accessory protein UreD	Family
C, G, K	IPR029754	Urease nickel binding site	Binding Site
C, G, K	IPR017950	Urease active site	Active Site
C, G, K	IPR006680	Amidohydrolase-related	Domain
C, G, K	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
C, G, K	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
C, G, K	IPR011612	Urease alpha-subunit, N-terminal domain	Domain
C, G, K	IPR050112	Urease Alpha Subunit	Family
C, G, K	IPR005848	Urease, alpha subunit	Family
C, G, K	IPR017951	Urease alpha subunit, C-terminal	Domain
B, F, J	IPR002019	Urease, beta subunit-like	Family
B, F, J	IPR050069	Urease subunit	Family
B, F, J	IPR036461	Urease, beta subunit superfamily	Homologous Superfamily
A, E, I	IPR050069	Urease subunit	Family
A, E, I	IPR012010	Urease, gamma subunit	Family
A, E, I	IPR002026	Urease, gamma/gamma-beta subunit	Family
A, E, I	IPR036463	Urease, gamma subunit 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.