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1,2-propanediol dehydration in roseburia inulinivorans; structural basis for substrate and enantiomer selectivity
Analyse 1,2-propanediol dehydration in roseburia inulinivorans; structural basis for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2A
- Type
- protein
- Length
- 1,673 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diol-dehydratase
- UniProt
- Q1A666
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diol-dehydratase | protein | 836 | 53% helix, 9% strand | Q1A666 |
| B | Diol-dehydratase | protein | 837 | 52% helix, 9% strand | Q1A666 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.77 | 0.82 | 82 | empty |
| 2 | 62 | 0.72 | 0.98 | 30 | empty |
| 3 | 61 | 0.72 | 0.98 | 31 | empty |
| 4 | 300 | 0.69 | 0.83 | 39 | empty |
| 5 | 388 | 0.65 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 530 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5I2A · 1,2-propanediol Dehydration in Roseburia inulinivorans; Structural Basis for Substrate… · 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 Q1A666
- Elsewhere: RCSB PDB 5I2A · PDBe 5I2A · UniProt Q1A666
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