Research workbench
Crystal structure of the steady-state-smx activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
Analyse Crystal structure of the steady-state-smx activated state of the light-driven… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YC0
- Type
- protein
- Length
- 1,345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium pumping rhodopsin
- UniProt
- N0DKS8
- Ligands
- LFA, OLA, RET, NA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Sodium pumping rhodopsin | protein | 269 | 77% helix, 3% strand | N0DKS8 |
Ligands and binding sites
- LFA · Eicosane · ligand · 21 copies · chains A, B, C, D, E
- OLA · Oleic acid · ligand · 8 copies · chains B, C, A, D, E
- RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 28 copies · chains A, B, E, C, D
- 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
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.75 | 0.93 | 24 | RET |
| 2 | 140 | 0.75 | 0.93 | 22 | RET |
| 3 | 141 | 0.75 | 0.92 | 25 | OLC, RET |
| 4 | 136 | 0.74 | 0.92 | 23 | RET |
| 5 | 151 | 0.73 | 0.91 | 24 | RET |
Interfaces
5 interfaces between chains.
- C–D · 1318 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1300 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1296 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1294 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (retinal Schiff base).
Compared structures
- 6YC0 · Crystal structure of the steady-state-SMX activated state of the light-driven sodium pump… · 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 6YC0 · PDBe 6YC0 · UniProt N0DKS8
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