Research workbench
Alpha-L-fucosidase alfc D200A mutant in complex with 4-nitrophenyl-a- L-fucopyranoside substrate
Analyse Alpha-L-fucosidase alfc D200A mutant in complex with 4-nitrophenyl-a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O1C
- Type
- protein
- Length
- 2,584 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alfc
- EC
- 3.2.1.51
- UniProt
- K0NB39
- Ligands
- JFZ
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Alfc (EC 3.2.1.51) | protein | 328 | 38% helix, 15% strand | K0NB39 |
| B | Alfc (EC 3.2.1.51) | protein | 323 | 38% helix, 15% strand | K0NB39 |
| C | Alfc (EC 3.2.1.51) | protein | 324 | 37% helix, 15% strand | K0NB39 |
| E | Alfc (EC 3.2.1.51) | protein | 322 | 37% helix, 15% strand | K0NB39 |
| F | Alfc (EC 3.2.1.51) | protein | 321 | 37% helix, 15% strand | K0NB39 |
| G | Alfc (EC 3.2.1.51) | protein | 322 | 38% helix, 15% strand | K0NB39 |
| H | Alfc (EC 3.2.1.51) | protein | 316 | 37% helix, 15% strand | K0NB39 |
Ligands and binding sites
- JFZ · 4-nitrophenyl 6-deoxy-alpha-L-galactopyranoside · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 795 | 0.77 | 0.81 | 87 | empty |
| 2 | 71 | 0.75 | 0.98 | 20 | empty |
| 3 | 59 | 0.73 | 0.99 | 14 | empty |
| 4 | 65 | 0.73 | 0.97 | 21 | empty |
| 5 | 61 | 0.73 | 0.98 | 15 | empty |
Interfaces
15 interfaces between chains.
- C–F · 1279 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 1279 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1277 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 1271 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 613 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6O1C · Alpha-L-fucosidase AlfC D200A mutant in complex with 4-nitrophenyl-a-L-fucopyranoside… · 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 6O1C · PDBe 6O1C · UniProt K0NB39
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