Research workbench
Pyruvate decarboyxlase from yeast (form B) complexed with pyruvamide
Analyse Pyruvate decarboyxlase from yeast (form B) complexed with pyruvamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QPB
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase (form B)
- EC
- 4.1.1.1
- UniProt
- P06169
- Ligands
- TPP, PYM, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate decarboxylase (form B) (EC 4.1.1.1) | protein | 555 | 39% helix, 18% strand | P06169 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- PYM · Pyruvamide · 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.81 | 0.87 | 74 | TPP |
| 2 | 479 | 0.80 | 0.88 | 71 | TPP, PYM |
| 3 | 92 | 0.71 | 0.94 | 23 | empty |
| 4 | 93 | 0.64 | 0.90 | 22 | empty |
| 5 | 468 | 0.63 | 0.77 | 74 | empty |
Interfaces
1 interface between chains.
- A–B · 3274 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1QPB · Pyruvate decarboyxlase from yeast (form B) complexed with pyruvamide · 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 0.97
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 P06169
- Elsewhere: RCSB PDB 1QPB · PDBe 1QPB · UniProt P06169
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