Research workbench
Pyruvate decarboxylase from zymobacter palmae
Analyse Pyruvate decarboxylase from zymobacter palmae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EUJ
- Type
- protein
- Length
- 13,322 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Zymobacter palmae
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- Q8KTX6
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.15 · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 555 | 39% helix, 18% strand | Q8KTX6 |
| E, I | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 556 | 39% helix, 19% strand | Q8KTX6 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, E, F, I, J, M, N, Q, R
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 | 811 | 0.88 | 0.91 | 119 | empty |
| 2 | 835 | 0.88 | 0.91 | 114 | empty |
| 3 | 866 | 0.88 | 0.90 | 136 | empty |
| 4 | 750 | 0.87 | 0.91 | 118 | empty |
| 5 | 763 | 0.85 | 0.88 | 85 | empty |
Interfaces
43 interfaces between chains.
- W–X · 4041 Ų buried · 71 hydrogen bonds · protein-protein
- U–V · 4029 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4017 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4011 Ų buried · 73 hydrogen bonds · protein-protein
- M–N · 4005 Ų buried · 70 hydrogen bonds · protein-protein
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 Q8KTX6
- Elsewhere: RCSB PDB 5EUJ · PDBe 5EUJ · UniProt Q8KTX6
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