Research workbench
Crystal structure of FMN-binding beta-glucuronidase from ruminococcus gnavus
Analyse Crystal structure of FMN-binding beta-glucuronidase from ruminococcus gnavus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MVG
- Type
- protein
- Length
- 1,910 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- Ligands
- FMN, CA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 637 | 16% helix, 38% strand | — |
| B | Beta-glucuronidase | protein | 636 | 16% helix, 37% strand | — |
| C | Beta-glucuronidase | protein | 637 | 17% helix, 37% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.70 | 0.76 | 63 | empty |
| 2 | 255 | 0.66 | 0.83 | 32 | FMN |
| 3 | 380 | 0.64 | 0.79 | 43 | empty |
| 4 | 382 | 0.63 | 0.78 | 45 | empty |
| 5 | 97 | 0.62 | 0.88 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–C · 960 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6MVG · Crystal structure of FMN-binding beta-glucuronidase from Ruminococcus gnavus · 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
- Elsewhere: RCSB PDB 6MVG · PDBe 6MVG
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