Research workbench
Crystal structure and functional studies of quinoprotein L-sorbose dehydrogenase from ketogulonicigenium vulgare Y25
Analyse Crystal structure and functional studies of quinoprotein L-sorbose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MH1
- Type
- protein
- Length
- 1,023 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorbose dehydrogenase
- UniProt
- E3F069
- Ligands
- PQQ, CA
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorbose dehydrogenase | protein | 509 | 3% helix, 39% strand | E3F069 |
| B | Sorbose dehydrogenase | protein | 514 | 3% helix, 39% strand | E3F069 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.50 | 0.84 | 22 | empty |
| 2 | 120 | 0.50 | 0.80 | 22 | PQQ, CA |
| 3 | 136 | 0.44 | 0.76 | 19 | empty |
| 4 | 51 | 0.34 | 0.79 | 20 | empty |
| 5 | 82 | 0.34 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1158 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4MH1 · Crystal structure and functional studies of quinoprotein L-sorbose dehydrogenase from… · 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 E3F069
- Elsewhere: RCSB PDB 4MH1 · PDBe 4MH1 · UniProt E3F069
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