Research workbench
The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from lactobacillus plantarum
Analyse The refined structures of a stabilized mutant and of wild-type pyruvate oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1POX
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate oxidase
- EC
- 1.2.3.3
- UniProt
- P37063
- Ligands
- TPP, FAD, MG, NA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate oxidase (EC 1.2.3.3) | protein | 585 | 43% helix, 16% strand | P37063 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.74 | 0.83 | 51 | FAD |
| 2 | 374 | 0.72 | 0.84 | 45 | FAD |
| 3 | 110 | 0.68 | 0.91 | 28 | MG, TPP |
| 4 | 111 | 0.67 | 0.90 | 27 | MG, TPP |
| 5 | 181 | 0.56 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1354 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1POX · The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P37063 · AlphaFold monomer V2.0 prediction for pyruvate oxidase (P37063) · 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 P37063
- Elsewhere: RCSB PDB 1POX · PDBe 1POX · UniProt P37063
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