MolNFT v1 · #159193 · protein
Alpha-L-fucosidase alfc D200A in complex with FUCA(1,6)GLCNAC
6OHE: “Alpha-L-fucosidase alfc D200A in complex with FUCA(1,6)GLCNAC”. X-ray diffraction, 2 ligands (NAG, FUC), 12 pockets (best druggability 0.73). MolNFT v1 #159193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OHE
- Type
- protein
- Length
- 1,289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alfc
- UniProt
- K0NB39
- Ligands
- NAG, FUC
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alfc | protein | 325 | 38% helix, 15% strand | K0NB39 |
| B | Alfc | protein | 322 | 38% helix, 15% strand | K0NB39 |
| C | Alfc | protein | 322 | 37% helix, 16% strand | K0NB39 |
| D | Alfc | protein | 320 | 38% helix, 16% strand | K0NB39 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 16 | empty |
| 2 | 279 | 0.64 | 0.81 | 30 | NAG, FUC |
| 3 | 261 | 0.59 | 0.79 | 37 | NAG, FUC |
| 4 | 270 | 0.59 | 0.79 | 34 | NAG, FUC |
| 5 | 232 | 0.56 | 0.78 | 35 | NAG, FUC |
Interfaces
3 interfaces between chains.
- A–C · 1263 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 296 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 147 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6OHE · Alpha-L-fucosidase AlfC D200A in complex with Fuca(1,6)GlcNAc · 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 K0NB39
- Elsewhere: RCSB PDB 6OHE · PDBe 6OHE · UniProt K0NB39
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