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Crystal structure of FMN-binding beta-glucuronidase from Roseburia hominis
Analyse Crystal structure of FMN-binding beta-glucuronidase from Roseburia hominis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MVH
- Type
- protein
- Length
- 2,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Roseburia hominis
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- A0A174HGC0
- Ligands
- FMN, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 639 | 18% helix, 37% strand | A0A174HGC0 |
| B, C | Beta-galactosidase (EC 3.2.1.23) | protein | 638 | 18% helix, 36% strand | A0A174HGC0 |
| D | Beta-galactosidase (EC 3.2.1.23) | protein | 305 | 21% helix, 17% strand | A0A174HGC0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
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 | 1066 | 0.84 | 0.85 | 87 | empty |
| 2 | 991 | 0.79 | 0.81 | 94 | empty |
| 3 | 577 | 0.78 | 0.85 | 43 | empty |
| 4 | 491 | 0.67 | 0.78 | 37 | empty |
| 5 | 318 | 0.62 | 0.79 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1114 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 955 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 646 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 427 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 116 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MVH · Crystal structure of FMN-binding beta-glucuronidase from roseburia hominis · 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 A0A174HGC0
- Elsewhere: RCSB PDB 6MVH · PDBe 6MVH · UniProt A0A174HGC0
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