Research workbench
Structure of diol dehydratase complexed with (R)-1,2-propanediol
Analyse Structure of diol dehydratase complexed with (R)-1,2-propanediol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UC5
- Type
- protein
- Length
- 1,731 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
- CNC, K, NH4
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Diol dehydrase alpha subunit (EC 4.2.1.28) | protein | 551 | 51% helix, 10% strand | Q59470 |
| B | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 178 | 33% helix, 22% strand | Q59471 |
| G, M | Diol dehydrase gamma subunit (EC 4.2.1.28) | protein | 137 | 66% helix, 1% strand | Q59472 |
| E | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 177 | 33% helix, 21% strand | Q59471 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B, L, E
- K · Potassium ion · metal · 2 copies · chains A, L
- NH4 · Ammonium ion · ion · 4 copies · chains A, L
- PGR · R-1,2-propanediol · additive · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.86 | 0.86 | 87 | PGR, CNC |
| 2 | 1190 | 0.85 | 0.86 | 82 | PGR, CNC |
| 3 | 165 | 0.72 | 0.90 | 31 | empty |
| 4 | 124 | 0.69 | 0.91 | 25 | empty |
| 5 | 160 | 0.66 | 0.87 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–L · 4308 Ų buried · 85 hydrogen bonds · protein-protein
- A–G · 2755 Ų buried · 49 hydrogen bonds · protein-protein
- L–M · 2707 Ų buried · 49 hydrogen bonds · protein-protein
- L–E · 1621 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1557 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1UC5 · Structure of diol dehydratase complexed with (R)-1,2-propanediol · 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 1UC5 · PDBe 1UC5 · UniProt Q59470 · UniProt Q59471 · UniProt Q59472
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