MolNFT v1 · #54228 · protein
Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in complex with an extended 9- fluorenone iminosugar inhibitor
2XII: “Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in complex with an extended…”. X-ray diffraction, 3 ligands (TYR, TA9, SO4), 6 pockets (best druggability 0.81). MolNFT v1 #54228 on GenesisL1: 3D…
- PDB
- 2XII
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- EC
- 3.2.1.51
- UniProt
- Q8A3I4
- Ligands
- TYR, TA9, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 438 | 32% helix, 23% strand | Q8A3I4 |
| B | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 439 | 32% helix, 23% strand | Q8A3I4 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- TA9 · 9-oxo-N-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-piperidin-2-yl]methyl]fluorene-1-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.81 | 0.82 | 86 | empty |
| 2 | 73 | 0.39 | 0.78 | 22 | TA9 |
| 3 | 56 | 0.35 | 0.78 | 18 | TA9, GOL |
| 4 | 64 | 0.29 | 0.74 | 18 | empty |
| 5 | 52 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1143 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2XII · Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron in… · the same entry in another collection · chain B against B, 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 Q8A3I4
- Elsewhere: RCSB PDB 2XII · PDBe 2XII · UniProt Q8A3I4
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