MolNFT v1 · #119194 · protein
6-phospho-beta-glucosidase
5FOO · 6-phospho-beta-D glycosidase: “6-phospho-beta-glucosidase”. X-ray diffraction, 3 ligands (JAZ, PO4, CL), 16 pockets (best druggability 0.76). MolNFT v1 #119194 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FOO
- Type
- protein
- Length
- 2,777 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-D glycosidase
- EC
- 3.2.1.21, 3.2.1.86
- UniProt
- Q99YP9
- Ligands
- JAZ, PO4, CL
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 6-phospho-beta-D glycosidase (EC 3.2.1.21, 3.2.1.86) | protein | 463 | 45% helix, 17% strand | Q99YP9 |
| F | 6-phospho-beta-D glycosidase (EC 3.2.1.21, 3.2.1.86) | protein | 462 | 45% helix, 17% strand | Q99YP9 |
Ligands and binding sites
- JAZ · 6-phosphocyclophellitol · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, C, B, F, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.76 | 0.83 | 53 | JAZ |
| 2 | 535 | 0.76 | 0.83 | 64 | JAZ, EDO |
| 3 | 573 | 0.76 | 0.82 | 54 | JAZ |
| 4 | 627 | 0.75 | 0.81 | 58 | JAZ, CL |
| 5 | 533 | 0.75 | 0.82 | 55 | JAZ |
Interfaces
6 interfaces between chains.
- A–C · 748 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 736 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 735 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 487 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5FOO · 6-phospho-beta-glucosidase · the same entry in another collection · 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 Q99YP9
- Elsewhere: RCSB PDB 5FOO · PDBe 5FOO · UniProt Q99YP9
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