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Crystal structure of NITRATE/NITRITE exchanger nark

Analyse Crystal structure of NITRATE/NITRITE exchanger nark in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JR9
Type: protein
Length: 833 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrite extrusion protein 1; Immunoglobulin gamma-2A, heavy chain; Immunoglobulin kappa…
UniProt: P10903
Ligands: GYP
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrite extrusion protein 1	protein	409	78% helix, 1% strand	P10903
H	Immunoglobulin gamma-2A, heavy chain	protein	213	7% helix, 52% strand	—
L	Immunoglobulin kappa, light chain	protein	211	6% helix, 53% strand	—

Ligands and binding sites

GYP · methyl alpha-D-glucopyranoside · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	317	0.60	0.78	38	empty
2	226	0.45	0.73	29	empty
3	106	0.44	0.79	20	empty
4	69	0.44	0.81	12	GYP
5	139	0.43	0.75	36	empty

Interfaces

3 interfaces between chains.

H–L · 1793 Å² buried · 7 hydrogen bonds · protein-protein
A–H · 577 Å² buried · 20 hydrogen bonds · protein-protein
A–L · 224 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4JR9 · Crystal structure of nitrate/nitrite exchanger NarK · the same entry in another collection · chain A against A, TM-score 1.00
P10903 · AlphaFold monomer V2.0 prediction for NITRATE/NITRITE transporter nark (P10903) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P10903
Elsewhere: RCSB PDB 4JR9 · PDBe 4JR9 · UniProt P10903

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