Research workbench
Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose
Analyse Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TR4
- Type
- protein
- Length
- 1,012 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F5/8 type C domain-containing protein
- UniProt
- A0A2N5PIE7
- Ligands
- FUC, FUL, CA, MG, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | F5/8 type C domain-containing protein | protein | 506 | 24% helix, 25% strand | A0A2N5PIE7 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.82 | 74 | MG |
| 2 | 882 | 0.70 | 0.75 | 72 | empty |
| 3 | 245 | 0.53 | 0.76 | 38 | FUL, FUC |
| 4 | 223 | 0.52 | 0.76 | 35 | FUC |
| 5 | 53 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6TR4 · Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose · 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 A0A2N5PIE7
- Elsewhere: RCSB PDB 6TR4 · PDBe 6TR4 · UniProt A0A2N5PIE7
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