Research workbench
Pyruvate decarboxylase from kluyveromyces lactis soaked with pyruvamide
Analyse Pyruvate decarboxylase from kluyveromyces lactis soaked with pyruvamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EFH
- Type
- protein
- Length
- 1,113 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- Q12629
- Ligands
- PY0, TPP, MG
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 557 | 38% helix, 18% strand | Q12629 |
| B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 556 | 40% helix, 18% strand | Q12629 |
Ligands and binding sites
- PY0 · (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate · ligand · 2 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.84 | 0.95 | 57 | TPP |
| 2 | 277 | 0.84 | 0.95 | 52 | TPP, MG |
| 3 | 51 | 0.61 | 0.93 | 19 | empty |
| 4 | 373 | 0.60 | 0.77 | 36 | empty |
| 5 | 319 | 0.58 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 3404 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6EFH · Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide · 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 0.96
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 6EFH · PDBe 6EFH · UniProt Q12629
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