MolNFT v1 · #122040 · protein
Structure of beta glucosidase 1A from thermotoga neapolitana, mutant E349A
5IDI · 1,4-beta-D-glucan glucohydrolase: “Structure of beta glucosidase 1A from thermotoga neapolitana, mutant E349A”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #122040 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IDI
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-beta-D-glucan glucohydrolase
- EC
- 3.2.1.74, 3.2.1.21
- UniProt
- B9K7M5
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-beta-D-glucan glucohydrolase (EC 3.2.1.74, 3.2.1.21) | protein | 443 | 46% helix, 18% strand | B9K7M5 |
| B | 1,4-beta-D-glucan glucohydrolase (EC 3.2.1.74, 3.2.1.21) | protein | 444 | 46% helix, 18% strand | B9K7M5 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.73 | 0.81 | 57 | ACT |
| 2 | 498 | 0.72 | 0.81 | 51 | ACT |
| 3 | 170 | 0.49 | 0.77 | 26 | empty |
| 4 | 112 | 0.46 | 0.79 | 12 | empty |
| 5 | 144 | 0.45 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1225 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5IDI · Structure of beta glucosidase 1A from Thermotoga neapolitana, mutant E349A · the same entry in another collection · chain A against A, TM-score 1.00
- B9K7M5 · AlphaFold monomer V2.0 prediction for 1,4-beta-D-glucan glucohydrolase (B9K7M5) · a predicted model of the same protein · 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 B9K7M5
- Elsewhere: RCSB PDB 5IDI · PDBe 5IDI · UniProt B9K7M5
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