Research workbench
X-ray structure of phenylpyruvate decarboxylase in complex with 3- deaza-thdp and phenylpyruvate
Analyse X-ray structure of phenylpyruvate decarboxylase in complex with 3- deaza-thdp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q5O
- Type
- protein
- Length
- 1,060 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylpyruvate decarboxylase
- EC
- 4.1.1.43
- UniProt
- P51852
- Ligands
- PPY, TPW, MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylpyruvate decarboxylase (EC 4.1.1.43) | protein | 529 | 41% helix, 17% strand | P51852 |
| B | Phenylpyruvate decarboxylase (EC 4.1.1.43) | protein | 531 | 40% helix, 18% strand | P51852 |
Ligands and binding sites
- PPY · 3-phenylpyruvic acid · ligand · 4 copies · chains A, B
- TPW · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.84 | 0.96 | 46 | PPY, MG, TPW |
| 2 | 290 | 0.81 | 0.91 | 53 | MG, TPW, PPY |
| 3 | 57 | 0.70 | 0.97 | 18 | PPY |
| 4 | 55 | 0.69 | 0.97 | 17 | PPY |
| 5 | 169 | 0.61 | 0.83 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 3519 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2Q5O · X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P51852 · AlphaFold monomer V2.0 prediction for indole-3-pyruvate decarboxylase (P51852) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P51852
- Elsewhere: RCSB PDB 2Q5O · PDBe 2Q5O · UniProt P51852
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