Research workbench
Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4 ångströms resolution
Analyse Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PYD
- 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
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 537 | 41% helix, 18% 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.86 | 0.87 | 145 | MG, TPP |
| 2 | 296 | 0.65 | 0.81 | 45 | empty |
| 3 | 270 | 0.58 | 0.78 | 42 | empty |
| 4 | 70 | 0.55 | 0.87 | 18 | empty |
| 5 | 83 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2838 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1PYD · Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at… · 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 0.98
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 1PYD · PDBe 1PYD · UniProt P06169
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