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Crystal structure of escherichia COLI-expressed halobacterium salinarum bacteriorhodopsin in the trimeric form
Analyse Crystal structure of escherichia COLI-expressed halobacterium salinarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XXJ
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- LFA, MPG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 229 | 77% helix, 5% strand | P02945 |
| B | Bacteriorhodopsin | protein | 224 | 75% helix, 5% strand | P02945 |
| C | Bacteriorhodopsin | protein | 228 | 75% helix, 5% strand | P02945 |
Ligands and binding sites
- LFA · Eicosane · ligand · 33 copies · chains A, B, C
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.77 | 0.78 | 90 | LFA |
| 2 | 357 | 0.72 | 0.83 | 34 | MPG |
| 3 | 390 | 0.70 | 0.81 | 36 | MPG |
| 4 | 396 | 0.68 | 0.81 | 38 | MPG |
| 5 | 67 | 0.35 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 741 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 725 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 719 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 4XXJ · Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin… · the same entry in another collection · chain A against A, TM-score 1.00
- P02945 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin (P02945) · a predicted model of the same protein · 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 P02945
- Elsewhere: RCSB PDB 4XXJ · PDBe 4XXJ · UniProt P02945
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