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The crystal structure of glycoside hydrolase bglx from P. aeruginosa in complex with 1-deoxynojirimycin
Analyse The crystal structure of glycoside hydrolase bglx from P. aeruginosa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5N
- Type
- protein
- Length
- 1,466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic beta-glucosidase
- UniProt
- Q9I311
- Ligands
- NOJ, MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Periplasmic beta-glucosidase | protein | 733 | 34% helix, 19% strand | Q9I311 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- PGE · Triethylene glycol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.86 | 0.96 | 37 | empty |
| 2 | 103 | 0.77 | 0.97 | 23 | empty |
| 3 | 102 | 0.76 | 0.97 | 22 | empty |
| 4 | 381 | 0.67 | 0.80 | 45 | empty |
| 5 | 282 | 0.64 | 0.81 | 30 | empty |
Interfaces
1 interface between chains.
- B–A · 3283 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 6R5N · The crystal structure of Glycoside Hydrolase BglX from P. aeruginosa in complex with… · the same entry in another collection · chain B against B, 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 Q9I311
- Elsewhere: RCSB PDB 6R5N · PDBe 6R5N · UniProt Q9I311
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