MolNFT v1 · #143334 · protein
Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-meo-N5PAN with pantothenate present in reaction
6AWJ: “Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-meo-N5PAN…”. X-ray diffraction, 2 ligands (ADP, N7G), 5 pockets (best druggability 0.80). MolNFT v1 #143334 on GenesisL1: 3D…
- PDB
- 6AWJ
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- A0A0D6HHM8
- Ligands
- ADP, N7G
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Type II pantothenate kinase (EC 2.7.1.33) | protein | 266 | 43% helix, 23% strand | A0A0D6HHM8 |
| B | Type II pantothenate kinase (EC 2.7.1.33) | protein | 263 | 43% helix, 22% strand | A0A0D6HHM8 |
| D | Type II pantothenate kinase (EC 2.7.1.33) | protein | 261 | 43% helix, 22% strand | A0A0D6HHM8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- N7G · (2R)-2-hydroxy-N-{3-[(5-methoxypentyl)amino]-3-oxopropyl}-3,3-dimethylbutanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.80 | 0.83 | 100 | N7G, ADP |
| 2 | 598 | 0.80 | 0.85 | 84 | ADP, N7G |
| 3 | 744 | 0.79 | 0.83 | 98 | N7G, ADP |
| 4 | 704 | 0.79 | 0.84 | 95 | ADP, N7G |
| 5 | 200 | 0.48 | 0.75 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2292 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2287 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AWJ · Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0D6HHM8
- Elsewhere: RCSB PDB 6AWJ · PDBe 6AWJ · UniProt A0A0D6HHM8
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