Research workbench
Crystal structure of type III pantothenate kinase from burkholderia thailandensis in complex with pantothenate and phosphate
Analyse Crystal structure of type III pantothenate kinase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O5F
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- Q2T1M2
- Ligands
- PAU, ATP, K, PO4, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III pantothenate kinase (EC 2.7.1.33) | protein | 258 | 37% helix, 25% strand | Q2T1M2 |
| B | Type III pantothenate kinase (EC 2.7.1.33) | protein | 248 | 38% helix, 26% strand | Q2T1M2 |
Ligands and binding sites
- PAU · Pantothenoic acid · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.76 | 0.84 | 56 | PAU, PO4, ATP |
| 2 | 390 | 0.74 | 0.84 | 56 | PAU, PO4, ATP |
| 3 | 57 | 0.43 | 0.82 | 16 | empty |
| 4 | 57 | 0.41 | 0.82 | 24 | empty |
| 5 | 63 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2228 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4O5F · Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2T1M2 · AlphaFold monomer V2.0 prediction for type III pantothenate kinase (Q2T1M2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q2T1M2
- Elsewhere: RCSB PDB 4O5F · PDBe 4O5F · UniProt Q2T1M2
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