Research workbench
Crystal structure of a probable glycerol dehydrogenase from sinorhizobium meliloti 1021
Analyse Crystal structure of a probable glycerol dehydrogenase from sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UHJ
- Type
- protein
- Length
- 2,842 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable glycerol dehydrogenase
- EC
- 1.1.1.6
- UniProt
- Q92MR2
- Ligands
- ZN, SE
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 357 | 54% helix, 13% strand | Q92MR2 |
| B, G | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 356 | 57% helix, 12% strand | Q92MR2 |
| C | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 355 | 57% helix, 13% strand | Q92MR2 |
| D | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 357 | 56% helix, 13% strand | Q92MR2 |
| E | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 355 | 56% helix, 13% strand | Q92MR2 |
| F | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 351 | 57% helix, 14% strand | Q92MR2 |
| H | Probable glycerol dehydrogenase (EC 1.1.1.6) | protein | 355 | 56% helix, 12% strand | Q92MR2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SE · Selenium atom · ion · 2 copies · chains E, H
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.76 | 0.81 | 76 | empty |
| 2 | 659 | 0.74 | 0.80 | 90 | GOL |
| 3 | 414 | 0.73 | 0.83 | 59 | GOL |
| 4 | 475 | 0.73 | 0.82 | 59 | GOL |
| 5 | 465 | 0.72 | 0.82 | 68 | GOL |
Interfaces
9 interfaces between chains.
- A–B · 1550 Ų buried · 38 hydrogen bonds · protein-protein
- E–H · 1505 Ų buried · 37 hydrogen bonds · protein-protein
- F–G · 1480 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1438 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 503 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 3UHJ · Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021 · 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 Q92MR2
- Elsewhere: RCSB PDB 3UHJ · PDBe 3UHJ · UniProt Q92MR2
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