MolNFT v1 · #170169 · protein
Crystal structure of the O-state of the light-driven sodium pump KR2 in the pentameric form, pH 8.0
6XYT · Sodium pumping rhodopsin: “Crystal structure of the O-state of the light-driven sodium pump KR2 in the pentameric form, pH 8.0”. X-ray diffraction, 3 ligands (LFA, OLA, NA), 9 pockets (best druggability 0.73). MolNFT v1 #170169 on…
- PDB
- 6XYT
- Type
- protein
- Length
- 1,355 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium pumping rhodopsin
- UniProt
- N0DKS8
- Ligands
- LFA, OLA, NA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Sodium pumping rhodopsin | protein | 270 | 76% helix, 3% strand | N0DKS8 |
| B | Sodium pumping rhodopsin | protein | 272 | 76% helix, 3% strand | N0DKS8 |
| C | Sodium pumping rhodopsin | protein | 273 | 75% helix, 3% strand | N0DKS8 |
Ligands and binding sites
- LFA · Eicosane · ligand · 24 copies · chains A, B, C, D, E
- OLA · Oleic acid · ligand · 14 copies · chains A, B, E, C, D
- NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 33 copies · chains A, B, E, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.73 | 0.77 | 65 | OLC |
| 2 | 577 | 0.73 | 0.80 | 78 | OLC |
| 3 | 537 | 0.72 | 0.80 | 60 | OLC |
| 4 | 556 | 0.71 | 0.79 | 66 | OLA, GOL |
| 5 | 572 | 0.71 | 0.78 | 51 | OLC, OLA |
Interfaces
5 interfaces between chains.
- B–C · 1319 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1314 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1303 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1297 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard).
Compared structures
- 6XYT · Crystal structure of the O-state of the light-driven sodium pump KR2 in the pentameric… · the same entry in another collection · chain A against A, TM-score 1.00
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 N0DKS8
- Elsewhere: RCSB PDB 6XYT · PDBe 6XYT · UniProt N0DKS8
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