Research workbench
The structure of pantothenate synthetase from burkholderia thailandensis
Analyse The structure of pantothenate synthetase from burkholderia thailandensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UK2
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- Q2T095
- Ligands
- AMP, MLT, CL
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantothenate synthetase (EC 6.3.2.1) | protein | 280 | 41% helix, 19% strand | Q2T095 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MLT · D-malate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.85 | 0.93 | 66 | AMP, MLT, EDO |
| 2 | 439 | 0.84 | 0.91 | 66 | AMP, MLT |
| 3 | 690 | 0.79 | 0.84 | 66 | CL |
| 4 | 82 | 0.39 | 0.77 | 16 | empty |
| 5 | 75 | 0.36 | 0.77 | 16 | CL |
Interfaces
1 interface between chains.
- A–B · 1313 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3UK2 · The structure of Pantothenate synthetase from Burkholderia thailandensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q2T095 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q2T095) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q2T095
- Elsewhere: RCSB PDB 3UK2 · PDBe 3UK2 · UniProt Q2T095
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