MolNFT v1 · #46219 · protein
Crystal structure of phenylpyruvate decarboxylase of azospirillum brasilense
2NXW · Phenyl-3-pyruvate decarboxylase: “Crystal structure of phenylpyruvate decarboxylase of azospirillum brasilense”. X-ray diffraction, 3 ligands (TPP, MG, CL), 8 pockets (best druggability 0.79). MolNFT v1 #46219 on GenesisL1: 3D…
- PDB
- 2NXW
- Type
- protein
- Length
- 1,066 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenyl-3-pyruvate decarboxylase
- EC
- 4.1.1.43
- UniProt
- P51852
- Ligands
- TPP, MG, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenyl-3-pyruvate decarboxylase (EC 4.1.1.43) | protein | 537 | 42% helix, 17% strand | P51852 |
| B | Phenyl-3-pyruvate decarboxylase (EC 4.1.1.43) | protein | 529 | 42% helix, 17% strand | P51852 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.79 | 0.83 | 77 | MG, TPP |
| 2 | 662 | 0.79 | 0.84 | 71 | MG, TPP |
| 3 | 393 | 0.67 | 0.80 | 44 | empty |
| 4 | 389 | 0.60 | 0.76 | 37 | empty |
| 5 | 116 | 0.51 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2976 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2NXW · Crystal structure of phenylpyruvate decarboxylase of Azospirillum brasilense · 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 0.99
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 2NXW · PDBe 2NXW · UniProt P51852
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