MolNFT v1 · #116937 · protein
Crystal structure of the GH1 beta-glucosidase from exiguobacterium antarcticum B7 in space group P21
5DT5: “Crystal structure of the GH1 beta-glucosidase from exiguobacterium antarcticum B7 in space group P21”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.80). MolNFT v1 #116937 on GenesisL1: 3D structure, binding…
- PDB
- 5DT5
- Type
- protein
- Length
- 3,532 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- K0A8J9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 444 | 43% helix, 16% strand | K0A8J9 |
| B, G | Beta-glucosidase (EC 3.2.1.21) | protein | 441 | 43% helix, 17% strand | K0A8J9 |
| C, D, H | Beta-glucosidase (EC 3.2.1.21) | protein | 443 | 43% helix, 18% strand | K0A8J9 |
| E | Beta-glucosidase (EC 3.2.1.21) | protein | 438 | 43% helix, 17% strand | K0A8J9 |
| F | Beta-glucosidase (EC 3.2.1.21) | protein | 439 | 43% helix, 17% strand | K0A8J9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D, E, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.80 | 0.81 | 98 | empty |
| 2 | 1024 | 0.79 | 0.81 | 101 | empty |
| 3 | 1043 | 0.79 | 0.81 | 104 | empty |
| 4 | 1102 | 0.79 | 0.81 | 108 | empty |
| 5 | 102 | 0.76 | 0.97 | 21 | empty |
Interfaces
15 interfaces between chains.
- A–B · 898 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 894 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 880 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 874 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 641 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5DT5 · Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in… · 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 K0A8J9
- Elsewhere: RCSB PDB 5DT5 · PDBe 5DT5 · UniProt K0A8J9
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