Research workbench
Crystal structure of phosphonopyruvate hydrolase complex with oxalate and mg++
Analyse Crystal structure of phosphonopyruvate hydrolase complex with oxalate and mg++ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DUA
- Type
- protein
- Length
- 283 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonopyruvate hydrolase
- UniProt
- Q84G06
- Ligands
- OXL, XYS, MG, NA, CL
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphonopyruvate hydrolase | protein | 283 | 47% helix, 14% strand | Q84G06 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · chains A
- XYS · alpha-D-xylopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · 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 | 259 | 0.54 | 0.76 | 32 | OXL, MG |
Compared structures
- 2DUA · Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++ · the same entry in another collection · chain A against A, TM-score 1.00
- Q84G06 · AlphaFold monomer V2.0 prediction for phosphonopyruvate hydrolase (Q84G06) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q84G06
- Elsewhere: RCSB PDB 2DUA · PDBe 2DUA · UniProt Q84G06
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