MolNFT v1 · #123388 · protein
Staphylococcus aureus type II pantothenate kinase in complex with a pantothenate analog
5JIC: “Staphylococcus aureus type II pantothenate kinase in complex with a pantothenate analog”. X-ray diffraction, 3 ligands (ADP, N7E, MG), 2 pockets (best druggability 0.63). MolNFT v1 #123388 on GenesisL1: 3D structure, binding sites…
- PDB
- 5JIC
- Type
- protein
- Length
- 269 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- Q8NVG0
- Ligands
- ADP, N7E, MG
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II pantothenate kinase (EC 2.7.1.33) | protein | 269 | 45% helix, 21% strand | Q8NVG0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- N7E · N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(5-methoxypentyl)-beta-alaninamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.63 | 0.80 | 46 | MG, ADP, N7E |
| 2 | 179 | 0.46 | 0.75 | 21 | empty |
Compared structures
- 5JIC · Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NVG0 · AlphaFold monomer V2.0 prediction for type II pantothenate kinase (Q8NVG0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8NVG0
- Elsewhere: RCSB PDB 5JIC · PDBe 5JIC · UniProt Q8NVG0
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