4XTN | pdb_00004xtn

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9

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
Membrane Protein Annotation: OPM
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	d4xtna_	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	d4xtnb1	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	d4xtnc1	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	d4xtnd1	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	d4xtne1	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)
F	d4xtnf1	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)
G	d4xtng1	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)
H	d4xtnh_	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)
I	d4xtni1	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)
J	d4xtnj1	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	SCOP2 Family	Bacteriorhodopsin-like	8071331	4001859	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2 (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)
F	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	G protein-coupled receptor-like	8071332	3000473	SCOP2B (2022-06-29)
J	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	e4xtnA1	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	e4xtnB1	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	e4xtnC1	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	e4xtnD1	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	e4xtnE1	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)
F	Bac_rhodopsin	e4xtnF1	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)
G	Bac_rhodopsin	e4xtnG1	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)
H	Bac_rhodopsin	e4xtnH1	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)
I	Bac_rhodopsin	e4xtnI1	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)
J	Bac_rhodopsin	e4xtnJ1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
B	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
C	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
D	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
E	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
F	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
G	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
H	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
I	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
J	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF01036	Bacteriorhodopsin-like protein (Bac_rhodopsin)	Bacteriorhodopsin-like protein	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, th ...	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR001425	Archaeal/bacterial/fungal rhodopsins	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	Microbial and algal rhodopsins

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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 A, B, C, D, E, F, G, H, I, J	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Bacterial, Algal, Viral, and Unusual Rhodopsins	KR2 light-driven Na⁺ pump, monomeric blue form at pH 4.3

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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.