Research workbench
2.1-ångström in situ mylar structure of bacteriorhodopsin from haloquadratum walsbyi (hwbr) at 100 K
Analyse 2.1-ångström in situ mylar structure of bacteriorhodopsin from haloquadratum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKH
- 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
- OLB, RET
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bacteriorhodopsin-I | protein | 228 | 76% helix, 4% strand | Q18DH8 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 3 copies · chains A, C, B
- RET · Retinal · ligand · 3 copies · chains A, B, C
- 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 | 126 | 0.81 | 0.98 | 23 | RET |
| 2 | 127 | 0.81 | 0.98 | 24 | RET |
| 3 | 120 | 0.80 | 0.98 | 22 | RET |
| 4 | 555 | 0.77 | 0.83 | 62 | OLC |
| 5 | 443 | 0.73 | 0.82 | 41 | OLB, OLC |
Interfaces
3 interfaces between chains.
- B–C · 576 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 561 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 540 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 5KKH · 2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi… · 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 C 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 5KKH · PDBe 5KKH · UniProt Q18DH8
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