Research workbench
Structure of the 6-phospho-beta glucosidase from thermotoga maritima at 2.55 ångström resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate
Analyse Structure of the 6-phospho-beta glucosidase from thermotoga maritima at 2.55… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UP6
- Type
- protein
- Length
- 3,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-glucosidase
- EC
- 3.2.1.6
- UniProt
- Q9X108
- Ligands
- NAD, G6P, MN, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 413 | 50% helix, 16% strand | Q9X108 |
| B | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 410 | 49% helix, 17% strand | Q9X108 |
| C | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 407 | 50% helix, 17% strand | Q9X108 |
| D | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 404 | 49% helix, 17% strand | Q9X108 |
| E | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 390 | 49% helix, 18% strand | Q9X108 |
| F | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 399 | 48% helix, 17% strand | Q9X108 |
| G | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 404 | 50% helix, 17% strand | Q9X108 |
| H | 6-phospho-beta-glucosidase (EC 3.2.1.6) | protein | 395 | 49% helix, 17% strand | Q9X108 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, G
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 5 copies · chains A, C, G
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.79 | 0.82 | 92 | NAD, MN, G6P |
| 2 | 386 | 0.79 | 0.88 | 58 | empty |
| 3 | 416 | 0.79 | 0.87 | 59 | empty |
| 4 | 489 | 0.78 | 0.85 | 44 | SO4 |
| 5 | 468 | 0.78 | 0.85 | 40 | SO4 |
Interfaces
9 interfaces between chains.
- A–B · 1731 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1713 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1701 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1690 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 934 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified (engineered).
Compared structures
- 1UP6 · Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9X108 · AlphaFold monomer V2.0 prediction for 6-phospho-beta-glucosidase bglt (Q9X108) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 Q9X108
- Elsewhere: RCSB PDB 1UP6 · PDBe 1UP6 · UniProt Q9X108
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