Research workbench
Structure of a NITRATE/NITRITE antiporter nark in nitrate-bound occluded state
Analyse Structure of a NITRATE/NITRITE antiporter nark in nitrate-bound occluded state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U4W
- Type
- protein
- Length
- 868 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NITRATE/NITRITE transporter nark
- UniProt
- P10903
- Ligands
- OLA, NO3
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NITRATE/NITRITE transporter nark | protein | 438 | 76% helix, 2% strand | P10903 |
| B | NITRATE/NITRITE transporter nark | protein | 430 | 78% helix, 2% strand | P10903 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 10 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.76 | 0.78 | 66 | OLA, OLC |
| 2 | 75 | 0.56 | 0.87 | 17 | empty |
| 3 | 131 | 0.47 | 0.78 | 23 | empty |
| 4 | 131 | 0.44 | 0.76 | 26 | empty |
| 5 | 106 | 0.43 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4U4W · Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state · 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 0.96
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 4U4W · PDBe 4U4W · UniProt P10903
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