MolNFT v1 · #143333 · protein
Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-N5PAN
6AWI: “Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-N5PAN”. X-ray diffraction, 2 ligands (ADP, C0D), 8 pockets (best druggability 0.84). MolNFT v1 #143333 on GenesisL1: 3D structure…
- PDB
- 6AWI
- Type
- protein
- Length
- 1,063 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, C0D
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Type II pantothenate kinase (EC 2.7.1.33) | protein | 266 | 44% helix, 23% strand | A0A0D6HHM8 |
| C | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 44% helix, 23% strand | A0A0D6HHM8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
- C0D · (2R)-2-hydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino) propyl]butanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.84 | 0.86 | 104 | ADP, C0D |
| 2 | 910 | 0.84 | 0.86 | 109 | ADP, C0D |
| 3 | 717 | 0.79 | 0.84 | 93 | ADP, C0D |
| 4 | 655 | 0.79 | 0.84 | 90 | ADP, C0D |
| 5 | 308 | 0.58 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2297 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2275 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1081 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6AWI · 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 6AWI · PDBe 6AWI · UniProt A0A0D6HHM8
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