Research workbench
Pyruvate decarboxylase from kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate
Analyse Pyruvate decarboxylase from kluyveromyces lactis in complex with the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VJY
- Type
- protein
- Length
- 2,248 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
- ALK, TPP, ALU, MG
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 562 | 42% helix, 17% strand | Q12629 |
Ligands and binding sites
- ALK · methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid · ligand · 8 copies · chains A, B, C, D
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- ALU · Methyl hydrogen (S)-acetylphosphonate · ligand · 3 copies · chains A, B, C
- 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
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.84 | 0.97 | 55 | TPP, ALK |
| 2 | 206 | 0.83 | 0.97 | 55 | TPP, ALK |
| 3 | 174 | 0.82 | 0.97 | 49 | TPP, MG, ALK |
| 4 | 444 | 0.81 | 0.89 | 80 | TPP, ALK |
| 5 | 506 | 0.64 | 0.76 | 61 | ALK |
Interfaces
4 interfaces between chains.
- A–B · 3815 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3792 Ų buried · 59 hydrogen bonds · protein-protein
- A–D · 490 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2VJY · Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue… · 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 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 Q12629
- Elsewhere: RCSB PDB 2VJY · PDBe 2VJY · UniProt Q12629
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