3LID | pdb_00003lid

Crystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8

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)
A	d3lida2	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	GGDEF family protein VP0354, C-terminal domain	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
A	d3lida1	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	GGDEF family protein VP0354, N-terminal domain	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
B	d3lidb2	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	GGDEF family protein VP0354, C-terminal domain	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)
B	d3lidb1	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	GGDEF family protein VP0354, N-terminal domain	(Vibrio parahaemolyticus ) [TaxId: 670 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Sensory domain-like	8035447	3001802	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sensory domain-like	8035449	3001802	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sensory domain-like	8035449	3001802	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sensory domain-like	8035447	3001802	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)
A	dCache_1_1	e3lidA2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: dCache_1_1	ECOD (1.6)
A	EUF08497	e3lidA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: EUF08497	ECOD (1.6)
B	dCache_1_1	e3lidB2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: dCache_1_1	ECOD (1.6)
B	EUF08497	e3lidB1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: EUF08497	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
B	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21623	Bacterial histidine kinase, sensor domain (HK_sensor_dom_bact)	Bacterial histidine kinase, sensor domain	This sensor domain is found in Histidine kinase from Vibrio parahaemolyticus. This domain shows an alpha-beta structure that folds into a double-PDC [1]. It is found associated with Pfam:PF13426 and Pfam:PF00990.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Putative sensory box/GGDEF family protein	transferase activity nucleotidyltransferase activity catalytic activity diguanylate cyclase activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein kinase activity protein kinase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion regulation of cell motility cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion regulation of cell motility negative regulation of biological process archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility regulation of locomotion negative regulation of cellular process negative regulation of cell motility bacterial-type flagellum-dependent cell motility cell motility negative regulation of bacterial-type flagellum-dependent cell motility locomotion cell adhesion involved in biofilm formation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms cell-substrate adhesion single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation cell adhesion involved in single-species biofilm formation cell adhesion single-species submerged biofilm formation	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000014	PAS domain	Domain
A, B	IPR050469	Bacterial Diguanylate Cyclase	Family
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR029151	Periplasmic sensor-like domain superfamily	Homologous Superfamily
A, B	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B	IPR048760	Histidine kinase VP0354-like, sensor domain	Domain
A, B	IPR000700	PAS-associated, C-terminal	Domain
A, B	IPR029787	Nucleotide cyclase	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.