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The crystal structure of glycoside hydrolase bglx inactive mutant D286N from P. aeruginosa in complex with cellobiose
Analyse The crystal structure of glycoside hydrolase bglx inactive mutant D286N from P.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5R
- Type
- protein
- Length
- 1,465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic beta-glucosidase
- UniProt
- Q9I311
- Ligands
- BGC, MG
- Pockets
- 16 · best druggability 0.86
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 | 732 | 35% helix, 19% strand | Q9I311 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains B, A
- PGE · Triethylene glycol · additive · 2 copies · chains B
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 | 301 | 0.86 | 0.96 | 35 | empty |
| 2 | 100 | 0.75 | 0.96 | 23 | empty |
| 3 | 87 | 0.75 | 0.97 | 21 | empty |
| 4 | 481 | 0.70 | 0.81 | 52 | empty |
| 5 | 333 | 0.66 | 0.81 | 33 | empty |
Interfaces
1 interface between chains.
- B–A · 3333 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 6R5R · 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 6R5R · PDBe 6R5R · UniProt Q9I311
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