MolNFT v1 · #91474 · protein
High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal B
4FEE: “High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin…”. X-ray diffraction, 5 ligands (PYR, FAD, TDM), 15 pockets (best druggability 0.78). MolNFT v1 #91474 on GenesisL1: 3D…
- PDB
- 4FEE
- Type
- protein
- Length
- 1,169 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate oxidase
- EC
- 1.2.3.3
- UniProt
- C6VNC6
- Ligands
- PYR, FAD, TDM, MG, PO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate oxidase (EC 1.2.3.3) | protein | 586 | 42% helix, 16% strand | C6VNC6 |
| B | Pyruvate oxidase (EC 1.2.3.3) | protein | 583 | 42% helix, 16% strand | C6VNC6 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TDM · 2-[(2E)-3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1-hydroxyethylidene)-4-methyl-2,3-dihydro-1,3-thiazol-5-yl]ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.78 | 0.83 | 65 | FAD, GOL |
| 2 | 371 | 0.71 | 0.83 | 45 | FAD |
| 3 | 104 | 0.70 | 0.93 | 29 | TDM, MG |
| 4 | 96 | 0.69 | 0.92 | 28 | TDM, MG |
| 5 | 137 | 0.61 | 0.85 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 1345 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4FEE · High-resolution structure of pyruvate oxidase in complex with reaction intermediate… · 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 C6VNC6
- Elsewhere: RCSB PDB 4FEE · PDBe 4FEE · UniProt C6VNC6
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