MolNFT v1 · #101891 · protein
Crystal structure of type III pantothenate kinase from burkholderia thailandensis in complex with pantothenate and phosphate
4O5F: “Crystal structure of type III pantothenate kinase from burkholderia thailandensis in complex with…”. X-ray diffraction, 5 ligands (PAU, ATP, K), 5 pockets (best druggability 0.76). MolNFT v1 #101891 on GenesisL1: 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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