Research workbench
Structure of diol dehydratase complexed with glycerol
Analyse Structure of diol dehydratase complexed with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AUJ
- Type
- protein
- Length
- 1,739 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diol dehydrase alpha subunit; Diol dehydrase beta subunit; Diol dehydrase gamma subunit
- EC
- 4.2.1.28
- UniProt
- Q59470, Q59471, Q59472
- Ligands
- B12, CA, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diol dehydrase alpha subunit (EC 4.2.1.28) | protein | 552 | 51% helix, 11% strand | Q59470 |
| B | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 179 | 32% helix, 22% strand | Q59471 |
| G | Diol dehydrase gamma subunit (EC 4.2.1.28) | protein | 139 | 62% helix, 1% strand | Q59472 |
| L | Diol dehydrase alpha subunit (EC 4.2.1.28) | protein | 551 | 50% helix, 11% strand | Q59470 |
| E | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 180 | 32% helix, 22% strand | Q59471 |
| M | Diol dehydrase gamma subunit (EC 4.2.1.28) | protein | 138 | 64% helix, 3% strand | Q59472 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B, L, E
- CA · Calcium ion · metal · 2 copies · chains A, L
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, G, L, E, M
- GOL · Glycerol · additive · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.86 | 0.87 | 84 | GOL, B12 |
| 2 | 1133 | 0.86 | 0.87 | 83 | GOL, B12 |
| 3 | 135 | 0.70 | 0.90 | 29 | empty |
| 4 | 137 | 0.70 | 0.90 | 28 | empty |
| 5 | 149 | 0.69 | 0.89 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–L · 4307 Ų buried · 90 hydrogen bonds · protein-protein
- A–G · 2778 Ų buried · 52 hydrogen bonds · protein-protein
- L–M · 2754 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1648 Ų buried · 22 hydrogen bonds · protein-protein
- L–E · 1646 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3AUJ · Structure of diol dehydratase complexed with glycerol · 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 Q59470
- Every structure of UniProt Q59471
- Every structure of UniProt Q59472
- Elsewhere: RCSB PDB 3AUJ · PDBe 3AUJ · UniProt Q59470 · UniProt Q59471 · UniProt Q59472
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