MolNFT v1 · #53623 · protein
Inhibition of the exo-beta-D-glucosaminidase csxa by a glucosamine-configured castanospermine and an amino- australine analogue
2X09: “Inhibition of the exo-beta-D-glucosaminidase csxa by a glucosamine-configured castanospermine and an amino…”. X-ray diffraction, 2 ligands (X09, CD), 20 pockets (best druggability 0.73). MolNFT v1 #53623 on GenesisL1: 3D structure…
- PDB
- 2X09
- Type
- protein
- Length
- 1,700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-D-glucosaminidase
- EC
- 3.2.1.165
- UniProt
- Q56F26
- Ligands
- X09, CD
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exo-beta-D-glucosaminidase (EC 3.2.1.165) | protein | 850 | 18% helix, 35% strand | Q56F26 |
Ligands and binding sites
- X09 · Amino-australine · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.73 | 0.83 | 39 | empty |
| 2 | 447 | 0.73 | 0.83 | 36 | empty |
| 3 | 442 | 0.65 | 0.78 | 55 | empty |
| 4 | 313 | 0.64 | 0.80 | 55 | empty |
| 5 | 259 | 0.63 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2X09 · Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured… · the same entry in another collection · chain A against A, TM-score 1.00
- Q56F26 · AlphaFold monomer V2.0 prediction for exo-beta-D-glucosaminidase (Q56F26) · a predicted model of the same protein · chain B 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 Q56F26
- Elsewhere: RCSB PDB 2X09 · PDBe 2X09 · UniProt Q56F26
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