Research workbench
Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
Analyse Crystal structure of the light-driven sodium pump KR2 in the pentameric form at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YC2
- Type
- protein
- Length
- 1,341 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium pumping rhodopsin
- UniProt
- N0DKS8
- Ligands
- LFA, OLA, ALA, NA
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Sodium pumping rhodopsin | protein | 268 | 77% helix, 3% strand | N0DKS8 |
| D | Sodium pumping rhodopsin | protein | 269 | 77% helix, 3% strand | N0DKS8 |
Ligands and binding sites
- LFA · Eicosane · ligand · 21 copies · chains A, B, E, C, D
- OLA · Oleic acid · ligand · 5 copies · chains A, B, C, D, E
- ALA · Alanine · ligand · chains C
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.71 | 0.77 | 83 | LFA, OLA |
| 2 | 567 | 0.70 | 0.78 | 46 | LFA |
| 3 | 560 | 0.70 | 0.78 | 46 | LFA |
| 4 | 588 | 0.70 | 0.78 | 42 | LFA |
| 5 | 558 | 0.69 | 0.78 | 42 | LFA |
Interfaces
5 interfaces between chains.
- B–C · 1327 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1320 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1317 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard).
Compared structures
- 6YC2 · Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room… · the same entry in another collection · chain B against B, 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 6YC2 · PDBe 6YC2 · UniProt N0DKS8
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