MolNFT v1 · #51861 · protein
Pyruvate decarboxylase from kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate
2VJY: “Pyruvate decarboxylase from kluyveromyces lactis in complex with the substrate analogue methyl…”. X-ray diffraction, 4 ligands (ALK, TPP, ALU), 16 pockets (best druggability 0.84). MolNFT v1 #51861 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.