MolNFT v1 · #18636 · protein
Crystal structure of the thiamin diphosphate dependent enzyme pyruvate decarboxylase from the yeast saccharomyces cerevisiae at 2.3 ångströms resolution
1PVD: “Crystal structure of the thiamin diphosphate dependent enzyme pyruvate decarboxylase from the yeast…”. X-ray diffraction, 2 ligands (TPP, MG), 4 pockets (best druggability 0.80). MolNFT v1 #18636 on GenesisL1: 3D structure, binding…
- PDB
- 1PVD
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- P06169
- Ligands
- TPP, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 537 | 40% helix, 19% strand | P06169 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.80 | 0.82 | 124 | MG, TPP |
| 2 | 870 | 0.76 | 0.80 | 119 | MG, TPP |
| 3 | 367 | 0.61 | 0.77 | 54 | empty |
| 4 | 114 | 0.52 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2863 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1PVD · Crystal structure of the thiamin diphosphate dependent enzyme pyruvate decarboxylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P06169 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase isozyme 1 (P06169) · a predicted model of the same protein · chain A 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 P06169
- Elsewhere: RCSB PDB 1PVD · PDBe 1PVD · UniProt P06169
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