MolNFT v1 · #157325 · protein
Crystal structure of FMN-binding beta-glucuronidase from facaelibacterium prausnitzii L2-6
6MVF · Beta-GALACTOSIDASE/BETA-glucuronidase: “Crystal structure of FMN-binding beta-glucuronidase from facaelibacterium prausnitzii L2-6”. X-ray diffraction, 1 ligand (FMN), 20 pockets (best druggability 0.70). MolNFT v1 #157325 on…
- PDB
- 6MVF
- Type
- protein
- Length
- 3,858 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-GALACTOSIDASE/BETA-glucuronidase
- EC
- 3.2.1.23
- UniProt
- D4K3H3
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-GALACTOSIDASE/BETA-glucuronidase (EC 3.2.1.23) | protein | 643 | 17% helix, 38% strand | D4K3H3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
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 | 479 | 0.70 | 0.81 | 46 | empty |
| 2 | 475 | 0.69 | 0.80 | 48 | empty |
| 3 | 781 | 0.69 | 0.76 | 85 | empty |
| 4 | 477 | 0.69 | 0.80 | 48 | empty |
| 5 | 445 | 0.68 | 0.80 | 43 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1245 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1243 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1243 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1242 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1235 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6MVF · Crystal structure of FMN-binding beta-glucuronidase from Facaelibacterium prausnitzii L2-6 · 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 D4K3H3
- Elsewhere: RCSB PDB 6MVF · PDBe 6MVF · UniProt D4K3H3
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