Research workbench
Structural insights into the pre-reaction state of pyruvate decarboxylase from zymomonas mobilis
Analyse Structural insights into the pre-reaction state of pyruvate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVG
- Type
- protein
- Length
- 2,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- P06672
- Ligands
- TPU, MG, F
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 565 | 40% helix, 18% strand | P06672 |
Ligands and binding sites
- TPU · 2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl trihydrogen diphosphate · ligand · 4 copies · chains A, B, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, E, F
- F · Fluoride ion · ion · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.82 | 0.97 | 41 | TPU, MG, F |
| 2 | 166 | 0.82 | 0.97 | 41 | TPU, MG |
| 3 | 166 | 0.81 | 0.97 | 43 | MG, TPU |
| 4 | 537 | 0.81 | 0.88 | 89 | empty |
| 5 | 166 | 0.81 | 0.97 | 36 | TPU, MG, F |
Interfaces
6 interfaces between chains.
- A–B · 4323 Ų buried · 75 hydrogen bonds · protein-protein
- E–F · 4317 Ų buried · 73 hydrogen bonds · protein-protein
- B–E · 1354 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 1347 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 714 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2WVG · Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- P06672 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (P06672) · 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 P06672
- Elsewhere: RCSB PDB 2WVG · PDBe 2WVG · UniProt P06672
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