Research workbench
Crystal structure of a novel pyruvate decarboxylase
Analyse Crystal structure of a novel pyruvate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MVE
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Vibrio vulnificus
- Molecule
- UPF0255 protein VV1_0328
- UniProt
- Q8DF91
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0255 protein VV1_0328 | protein | 396 | 48% helix, 15% strand | Q8DF91 |
| B | UPF0255 protein VV1_0328 | protein | 395 | 48% helix, 16% strand | Q8DF91 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.80 | 0.87 | 71 | EDO |
| 2 | 499 | 0.74 | 0.82 | 65 | SO4 |
| 3 | 512 | 0.64 | 0.76 | 71 | EDO, SO4 |
| 4 | 170 | 0.55 | 0.80 | 30 | EDO |
| 5 | 59 | 0.48 | 0.85 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 980 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 Q8DF91
- Elsewhere: RCSB PDB 3MVE · PDBe 3MVE · UniProt Q8DF91
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