1OXK | pdb_00001oxk

Complex between YPD1 and SLN1 response regulator domain in space group P3(2)

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)
L	d1oxkl_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J	d1oxkj_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d1oxkh_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1oxkf_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1oxkd_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1oxkb_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator Sin1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K	d1oxkk_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I	d1oxki_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d1oxkg_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1oxke_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1oxkc_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1oxka_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8036545	3001156	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	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)
L	B12-binding	e1oxkL1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
J	B12-binding	e1oxkJ1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
H	B12-binding	e1oxkH1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
F	B12-binding	e1oxkF1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
D	B12-binding	e1oxkD1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
B	B12-binding	e1oxkB1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v295)
K	Apolipoprotein	e1oxkK1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)
I	Apolipoprotein	e1oxkI1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)
G	Apolipoprotein	e1oxkG1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)
E	Apolipoprotein	e1oxkE1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)
C	Apolipoprotein	e1oxkC1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)
A	Apolipoprotein	e1oxkA1	A: alpha arrays	X: Urease, gamma-subunit	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: Apolipoprotein	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
J	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
H	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
K	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)
I	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)
G	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)
E	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)
C	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)
A	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain
A, C, E, G, I A, C, E, G, I, K	PF01627	Hpt domain (Hpt)	Hpt domain	The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has bee ...	The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined [1]. The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to contain a binding surface for Ssk1p (response regulator receiver domain containing protein Pfam:PF00072) [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	SLN1	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 molecular transducer activity molecular sensor activity transmembrane signaling receptor activity signaling receptor activity molecular function regulator activity osmosensor activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups phosphorelay sensor kinase activity cation binding metal ion binding histidine phosphotransfer 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 osmosensory signaling via phosphorelay pathway cellular response to chemical stress cellular response to environmental stimulus 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 osmosensory signaling via phosphorelay pathway cellular response to chemical stress cellular response to environmental stimulus osmosensory signaling pathway cellular response to stress response to stress response to osmotic stress cellular response to osmotic stress cellular response to chemical stimulus response to chemical response to abiotic stimulus cellular response to abiotic stimulus	cell periphery cellular anatomical structure plasma membrane membrane
A, C, E, G, I A, C, E, G, I, K	Ypd1p	transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein histidine kinase binding protein binding binding kinase binding enzyme binding protein kinase binding molecular transducer activity catalytic activity, acting on a protein kinase activity histidine phosphotransfer kinase activity protein kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein histidine kinase binding protein binding binding kinase binding enzyme binding protein kinase binding molecular transducer activity catalytic activity, acting on a protein kinase activity histidine phosphotransfer kinase activity protein kinase activity phosphotransferase activity, alcohol group as acceptor	cellular response to stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway response to stimulus signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress cellular response to stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway response to stimulus signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress regulation of biological process phosphorelay signal transduction system biological regulation cellular response to osmotic stress cellular response to chemical stimulus response to chemical cellular process response to abiotic stimulus cellular response to abiotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR011006	CheY-like superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR001789	Signal transduction response regulator, receiver domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR003660	HAMP domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR005467	Histidine kinase domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR045871	Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1	Family
A, C, E, G, I A, C, E, G, I, K	IPR036641	HPT domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR008207	Signal transduction histidine kinase, phosphotransfer (Hpt) domain	Domain

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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.