MolNFT v1 · #51574 · protein
Holostructure of pyruvate decarboxylase from acetobacter pasteurianus
2VBI: “Holostructure of pyruvate decarboxylase from acetobacter pasteurianus”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #51574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VBI
- Type
- protein
- Length
- 4,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- Q8L388
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 554 | 38% helix, 18% strand | Q8L388 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.89 | 0.91 | 130 | empty |
| 2 | 600 | 0.85 | 0.91 | 82 | empty |
| 3 | 757 | 0.85 | 0.88 | 87 | empty |
| 4 | 509 | 0.84 | 0.90 | 60 | empty |
| 5 | 662 | 0.83 | 0.88 | 62 | empty |
Interfaces
16 interfaces between chains.
- C–D · 3950 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3946 Ų buried · 67 hydrogen bonds · protein-protein
- G–H · 3943 Ų buried · 65 hydrogen bonds · protein-protein
- E–F · 3938 Ų buried · 66 hydrogen bonds · protein-protein
- A–D · 1541 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2VBI · Holostructure of pyruvate decarboxylase from Acetobacter pasteurianus · the same entry in another collection · 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 Q8L388
- Elsewhere: RCSB PDB 2VBI · PDBe 2VBI · UniProt Q8L388
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