MolNFT v1 · #52716 · protein
Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide
2W93 · Pyruvate decarboxylase isozyme 1: “Crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the…”. X-ray diffraction, 3 ligands (PY0, TPP, MG), 18 pockets (best druggability 0.82).…
- PDB
- 2W93
- Type
- protein
- Length
- 2,225 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
- PY0, TPP, MG
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) | protein | 544 | 42% helix, 18% strand | P06169 |
| B, D | Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) | protein | 562 | 41% helix, 17% strand | P06169 |
| C | Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) | protein | 557 | 42% helix, 18% strand | P06169 |
Ligands and binding sites
- PY0 · (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate · 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
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.82 | 0.97 | 46 | TPP, PY0 |
| 2 | 154 | 0.81 | 0.97 | 35 | TPP, MG, PY0 |
| 3 | 470 | 0.79 | 0.86 | 78 | TPP, MG, PY0 |
| 4 | 675 | 0.75 | 0.81 | 84 | TPP |
| 5 | 441 | 0.63 | 0.77 | 76 | PY0 |
Interfaces
4 interfaces between chains.
- C–D · 3389 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3355 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 509 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2W93 · Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q 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 B 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 2W93 · PDBe 2W93 · UniProt P06169
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