MolNFT v1 · #122577 · protein
2.2-ångström in meso crystal structure of haloquadratum walsbyi bacteriorhodopsin (hwbr) from octylglucoside (og) detergent micelles
5ITE · Bacteriorhodopsin-I: “2.2-ångström in meso crystal structure of haloquadratum walsbyi bacteriorhodopsin (hwbr) from octylglucoside…”. X-ray diffraction, 2 ligands (RET, OLB), 7 pockets (best druggability 0.81). MolNFT v1 #122577 on…
- PDB
- 5ITE
- Type
- protein
- Length
- 684 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin-I
- UniProt
- Q18DH8
- Ligands
- RET, OLB
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bacteriorhodopsin-I | protein | 228 | 77% helix, 4% strand | Q18DH8 |
Ligands and binding sites
- RET · Retinal · ligand · 3 copies · chains A, B, C
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 3 copies · chains A, C, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 24 | RET |
| 2 | 125 | 0.80 | 0.98 | 24 | RET |
| 3 | 124 | 0.79 | 0.97 | 23 | RET |
| 4 | 629 | 0.79 | 0.83 | 67 | OLC |
| 5 | 598 | 0.78 | 0.84 | 59 | OLB, OLC |
Interfaces
3 interfaces between chains.
- B–C · 587 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 549 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 5ITE · 2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q18DH8 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin-I (Q18DH8) · a predicted model of the same protein · chain B 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 Q18DH8
- Elsewhere: RCSB PDB 5ITE · PDBe 5ITE · UniProt Q18DH8
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