Research workbench
Functional and structural characterization of pyruvate decarboxylase from gluconoacetobacter diazotrophicus
Analyse Functional and structural characterization of pyruvate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COK
- Type
- protein
- Length
- 1,097 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- A9H275
- Ligands
- TPP, MG, SO4
- Pockets
- 12 · best druggability 0.81
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 | 548 | 39% helix, 18% strand | A9H275 |
| B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 549 | 39% helix, 18% strand | A9H275 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.81 | 0.98 | 40 | TPP |
| 2 | 153 | 0.81 | 0.97 | 41 | TPP, MG |
| 3 | 266 | 0.63 | 0.81 | 60 | empty |
| 4 | 170 | 0.55 | 0.80 | 35 | empty |
| 5 | 105 | 0.48 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3908 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 4COK · Functional and Structural Characterization of Pyruvate decarboxylase from… · 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 A9H275
- Elsewhere: RCSB PDB 4COK · PDBe 4COK · UniProt A9H275
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