MolNFT v1 · #89198 · protein
Crystal structure of the D248A mutant of 2-pyrone-4,6-dicarboxylic acid hydrolase from sphingomonas paucimobilis complexed with substrate at pH 6.5
4DI9 · 2-pyrone-4,6-dicarbaxylate hydrolase: “Crystal structure of the D248A mutant of 2-pyrone-4,6-dicarboxylic acid hydrolase from sphingomonas…”. X-ray diffraction, 1 ligand (0GY), 1 pocket (best druggability 0.58). MolNFT v1 #89198 on…
- PDB
- 4DI9
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-pyrone-4,6-dicarbaxylate hydrolase
- UniProt
- O87170
- Ligands
- 0GY
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-pyrone-4,6-dicarbaxylate hydrolase | protein | 293 | 41% helix, 14% strand | O87170 |
Ligands and binding sites
- 0GY · (1E,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylic acid · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.58 | 0.82 | 24 | empty |
Compared structures
- 4DI9 · CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM… · the same entry in another collection · chain A against A, TM-score 1.00
- O87170 · AlphaFold monomer V2.0 prediction for 2-pyrone-4,6-dicarboxylate hydrolase (O87170) · a predicted model of the same protein · 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 O87170
- Elsewhere: RCSB PDB 4DI9 · PDBe 4DI9 · UniProt O87170
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