MolNFT v1 · #162338 · protein
The crystal structure of glycoside hydrolase bglx inactive mutant D286N from P. aeruginosa in complex with xylotriose
6R5V · Periplasmic beta-glucosidase: “The crystal structure of glycoside hydrolase bglx inactive mutant D286N from P. aeruginosa in complex with…”. X-ray diffraction, 2 ligands (XYP, MG), 17 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6R5V
- Type
- protein
- Length
- 1,463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic beta-glucosidase
- UniProt
- Q9I311
- Ligands
- XYP, MG
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Periplasmic beta-glucosidase | protein | 733 | 34% helix, 20% strand | Q9I311 |
| A | Periplasmic beta-glucosidase | protein | 730 | 34% helix, 19% strand | Q9I311 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.85 | 0.96 | 35 | empty |
| 2 | 90 | 0.75 | 0.97 | 21 | empty |
| 3 | 89 | 0.74 | 0.96 | 23 | empty |
| 4 | 468 | 0.70 | 0.81 | 50 | empty |
| 5 | 430 | 0.62 | 0.77 | 50 | XYP |
Interfaces
1 interface between chains.
- B–A · 3336 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 6R5V · The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P.… · 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 6R5V · PDBe 6R5V · UniProt Q9I311
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