Research workbench
X-ray structure of phenylpyruvate decarboxylase in complex with 3- deaza-thdp and 5-phenyl-2-oxo-valeric acid
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
- 2Q5Q
- Type
- protein
- Length
- 1,068 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
- KPV, TPW, MG
- Pockets
- 12 · best druggability 0.80
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 | 533 | 41% helix, 17% strand | P51852 |
| B | Phenylpyruvate decarboxylase (EC 4.1.1.43) | protein | 535 | 42% helix, 17% strand | P51852 |
Ligands and binding sites
- KPV · 5-phenyl-2-keto-valeric 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 · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.80 | 0.86 | 69 | KPV, MG, TPW |
| 2 | 360 | 0.79 | 0.89 | 59 | MG, TPW, KPV |
| 3 | 105 | 0.62 | 0.88 | 24 | KPV |
| 4 | 148 | 0.62 | 0.85 | 36 | KPV |
| 5 | 153 | 0.61 | 0.84 | 32 | GOL |
Interfaces
1 interface between chains.
- A–B · 3448 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2Q5Q · 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 B against A, TM-score 0.96
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 2Q5Q · PDBe 2Q5Q · UniProt P51852
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