MolNFT v1 · #150220 · protein
Alpha-L-fucosidase isoenzyme 1 from paenibacillus thiaminolyticus
6GN6: “Alpha-L-fucosidase isoenzyme 1 from paenibacillus thiaminolyticus”. X-ray diffraction, 2 ligands (GLC, NA), 20 pockets (best druggability 0.81). MolNFT v1 #150220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GN6
- Type
- protein
- Length
- 2,537 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- EC
- 3.2.1.51
- UniProt
- E3PQQ9
- Ligands
- GLC, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 421 | 29% helix, 20% strand | E3PQQ9 |
| D | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 425 | 29% helix, 20% strand | E3PQQ9 |
| F | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 428 | 30% helix, 20% strand | E3PQQ9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 22 copies · chains A, C, E, D, F, B
- NA · Sodium ion · metal · 2 copies
- PGE · Triethylene glycol · additive · 10 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, A, E, F
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.81 | 0.86 | 88 | empty |
| 2 | 774 | 0.80 | 0.83 | 95 | empty |
| 3 | 548 | 0.78 | 0.84 | 79 | empty |
| 4 | 789 | 0.70 | 0.77 | 86 | GLC |
| 5 | 704 | 0.69 | 0.77 | 77 | GLC, PEG |
Interfaces
9 interfaces between chains.
- C–D · 1746 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1746 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1741 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 574 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 560 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6GN6 · Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus · the same entry in another collection · chain F against F, 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 E3PQQ9
- Elsewhere: RCSB PDB 6GN6 · PDBe 6GN6 · UniProt E3PQQ9
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