4JRE | pdb_00004jre

Crystal structure of nitrate/nitrite exchanger NarK with nitrite bound

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth L]	d4jrel2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth L]	d4jrel1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4jrec2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4jrec1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth H]	d4jreh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4jreb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth L]	PGM_PMM_IV	e4jreL1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PGM_PMM_IV	ECOD (v294.1)
C	PGM_PMM_IV	e4jreC1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PGM_PMM_IV	ECOD (v294.1)
E [auth H]	PGM_PMM_IV	e4jreH1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PGM_PMM_IV	ECOD (v294.1)
B	PGM_PMM_IV	e4jreB1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PGM_PMM_IV	ECOD (v294.1)
D	HTH_24	e4jreD1	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (v294.1)
A	AsnC_trans_reg_3	e4jreA5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: AsnC_trans_reg_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	1.20.1250.20	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
A	1.20.1250.20	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C, F [auth L]	IMMUNOGLOBULIN	L-KAPPA	Mus musculus (house mouse)	IGKV19-9301, IGKV19-9302, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202611-0)
B, E [auth H]	IMMUNOGLOBULIN	VH-CH1	Mus musculus (house mouse)	IGHV9-302, IGHV9-3-101, IGHJ401, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, F [auth L]	Light Chain	IGKV19	Kappa	nitrite extrusion protein 1	SAbDab (2026-03-27)
B, E [auth H]	Heavy Chain	IGHV9	-	nitrite extrusion protein 1	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF07690	Major Facilitator Superfamily (MFS_1)	Major Facilitator Superfamily	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth L]	Immunoglobulin Kappa, Light chain	-	-	-
B, E [auth H]	Immunoglobulin Gamma-2a, Heavy chain	-	-	-
A, D	Nitrite extrusion protein 1	antiporter activity active transmembrane transporter activity transporter activity transmembrane transporter activity solute:inorganic anion antiporter activity secondary active transmembrane transporter activity nitrite transmembrane transporter activity nitrate transmembrane transporter activity	nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process catabolic process nitrate catabolic process localization nitrogen compound transport transport nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process catabolic process nitrate catabolic process localization nitrogen compound transport transport establishment of localization nitrite transport inorganic anion transport transmembrane transport nitrate transmembrane transport nitrate import	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR044772	Nitrate transporter	Family
A, D	IPR004737	Nitrate transporter NarK/NarU-like	Family
A, D	IPR011701	Major facilitator superfamily	Family
A, D	IPR036259	MFS transporter superfamily	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Major Facilitator Superfamily (MFS) Transporters	NarK nitrate/nitrite exchanger

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.