Research workbench
Staphylococcus aureus type II pantothenate kinase in complex with nucleotides and pantothenate analog deoxy-N190PAN
Analyse Staphylococcus aureus type II pantothenate kinase in complex with nucleotides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AWG
- Type
- protein
- Length
- 1,061 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
- C0G, ATP, ADP
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Type II pantothenate kinase (EC 2.7.1.33) | protein | 266 | 42% helix, 23% strand | A0A0D6HHM8 |
| B | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 43% helix, 23% strand | A0A0D6HHM8 |
| D | Type II pantothenate kinase (EC 2.7.1.33) | protein | 264 | 43% helix, 22% strand | A0A0D6HHM8 |
Ligands and binding sites
- C0G · (2R)-N-(3-{[(2H-1,3-benzodioxol-5-yl)methyl]amino}-3-oxopropyl)-2-hydroxy-3,3-dimethylbutanamide · ligand · 4 copies · chains A, B, C, D
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, 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 | 987 | 0.85 | 0.86 | 107 | ATP, C0G |
| 2 | 944 | 0.84 | 0.85 | 100 | ATP, C0G |
| 3 | 718 | 0.80 | 0.84 | 92 | C0G, ADP |
| 4 | 655 | 0.79 | 0.84 | 86 | C0G, ADP |
| 5 | 333 | 0.62 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2287 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2274 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6AWG · Staphylococcus aureus Type II pantothenate kinase in complex with nucleotides and… · 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 6AWG · PDBe 6AWG · UniProt A0A0D6HHM8
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