MolNFT v1 · #51867 · protein
Crystal structure of pyruvate decarboxylase from kluyveromyces lactis
2VK4: “Crystal structure of pyruvate decarboxylase from kluyveromyces lactis”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.90). MolNFT v1 #51867 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VK4
- Type
- protein
- Length
- 2,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- Q12629
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 560 | 41% helix, 18% strand | Q12629 |
| B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 557 | 40% helix, 18% strand | Q12629 |
| C | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 555 | 41% helix, 19% strand | Q12629 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.90 | 0.95 | 119 | TPP, MG |
| 2 | 297 | 0.84 | 0.94 | 49 | TPP |
| 3 | 847 | 0.83 | 0.86 | 117 | empty |
| 4 | 224 | 0.83 | 0.96 | 51 | TPP, MG |
| 5 | 273 | 0.72 | 0.86 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3390 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3382 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 872 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 732 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VK4 · Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis · the same entry in another collection · chain A against A, TM-score 1.00
- Q12629 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (Q12629) · a predicted model of the same protein · chain A 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 Q12629
- Elsewhere: RCSB PDB 2VK4 · PDBe 2VK4 · UniProt Q12629
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