Research workbench
Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate
Analyse Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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