MolNFT v1 · #51864 · protein
Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate
2VK1 · Pyruvate decarboxylase isozyme 1: “Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its…”. X-ray diffraction, 3 ligands (PYR, TPP, MG), 17 pockets (best druggability 0.82). MolNFT…
- PDB
- 2VK1
- Type
- protein
- Length
- 2,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase isozyme 1
- EC
- 4.1.1.1
- UniProt
- P06169
- Ligands
- PYR, TPP, MG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) | protein | 562 | 41% helix, 17% strand | P06169 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 8 copies · chains A, B, C, D
- 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
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.82 | 0.97 | 43 | TPP, MG, PYR |
| 2 | 150 | 0.81 | 0.97 | 39 | TPP, PYR |
| 3 | 148 | 0.80 | 0.97 | 41 | TPP, PYR |
| 4 | 143 | 0.80 | 0.97 | 38 | TPP, PYR |
| 5 | 211 | 0.63 | 0.83 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3780 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3751 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 544 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 486 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2VK1 · Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in… · 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 1.00
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 2VK1 · PDBe 2VK1 · UniProt P06169
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