MolNFT v1 · #84108 · protein
Crystal structure of the light-driven sodium pump KR2 in acidic state
3X3B · Sodium pumping rhodopsin: “Crystal structure of the light-driven sodium pump KR2 in acidic state”. X-ray diffraction, 2 ligands (OLA, RET), 1 pocket (best druggability 0.73). MolNFT v1 #84108 on GenesisL1: 3D structure, binding…
- PDB
- 3X3B
- Type
- protein
- Length
- 271 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium pumping rhodopsin
- UniProt
- N0DKS8
- Ligands
- OLA, RET
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium pumping rhodopsin | protein | 271 | 76% helix, 3% strand | N0DKS8 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 3 copies · chains A
- RET · Retinal · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.73 | 0.92 | 24 | RET |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 3X3B · Crystal structure of the light-driven sodium pump KR2 in acidic state · 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 3X3B · PDBe 3X3B · UniProt N0DKS8
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