MolNFT v1 · #36224 · protein
Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin diphosphate
2EZ8: “Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin diphosphate”. X-ray diffraction, 5 ligands (TDL, FAD, PYR), 14 pockets (best druggability 0.78). MolNFT v1 #36224 on GenesisL1: 3D structure…
- PDB
- 2EZ8
- 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
- TDL, FAD, PYR, MG, NA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate oxidase (EC 1.2.3.3) | protein | 585 | 42% helix, 16% strand | P37063 |
Ligands and binding sites
- TDL · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1-carboxy-1-hydroxyethyl)-5-(2-{[hydroxy(phosphonooxy) phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.78 | 0.86 | 59 | FAD |
| 2 | 257 | 0.70 | 0.85 | 42 | FAD |
| 3 | 110 | 0.68 | 0.91 | 30 | MG, TDL |
| 4 | 104 | 0.66 | 0.90 | 30 | MG, TDL |
| 5 | 153 | 0.60 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1358 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2EZ8 · Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin… · 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 2EZ8 · PDBe 2EZ8 · UniProt P37063
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