6YC2 | pdb_00006yc2

Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6yc2a_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Dokdonia eikasta ) [TaxId: 308116 ],	SCOPe (2.08)
B	d6yc2b_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Dokdonia eikasta ) [TaxId: 308116 ],	SCOPe (2.08)
C	d6yc2c_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Dokdonia eikasta ) [TaxId: 308116 ],	SCOPe (2.08)
D	d6yc2d_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Dokdonia eikasta ) [TaxId: 308116 ],	SCOPe (2.08)
E	d6yc2e_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Dokdonia eikasta ) [TaxId: 308116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	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	Bac_rhodopsin	e6yc2A1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
B	Bac_rhodopsin	e6yc2B1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
C	Bac_rhodopsin	e6yc2C1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
D	Bac_rhodopsin	e6yc2D1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
E	Bac_rhodopsin	e6yc2E1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Sodium pumping rhodopsin	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR001425	Archaeal/bacterial/fungal rhodopsins	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Bacterial, Algal, Viral, and Unusual Rhodopsins	KR2 light-driven Na⁺ pump, pentameric form in O-state, pH 8

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E	LYR	Parent Component: LYS RESID: AA0120 PSI-MOD : N6-retinylidene-L-lysine MOD:00129

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.