MolNFT v1 · #147401 · protein
Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-N7-pan
6EBV: “Staphylococcus aureus type II pantothenate kinase in complex with ADP and pantothenate analog deoxy-N7-pan”. X-ray diffraction, 2 ligands (ADP, 27Q), 7 pockets (best druggability 0.85). MolNFT v1 #147401 on GenesisL1: 3D structure…
- PDB
- 6EBV
- Type
- protein
- Length
- 1,064 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, 27Q
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type II pantothenate kinase (EC 2.7.1.33) | protein | 266 | 43% helix, 23% strand | A0A0D6HHM8 |
| C | Type II pantothenate kinase (EC 2.7.1.33) | protein | 267 | 43% helix, 22% strand | A0A0D6HHM8 |
| D | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 42% helix, 24% strand | A0A0D6HHM8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 27Q · N-heptyl-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.85 | 0.87 | 102 | ADP, 27Q |
| 2 | 840 | 0.84 | 0.86 | 102 | ADP, 27Q |
| 3 | 720 | 0.80 | 0.84 | 91 | ADP, 27Q |
| 4 | 738 | 0.79 | 0.83 | 93 | ADP, 27Q |
| 5 | 349 | 0.62 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2363 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2344 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1149 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6EBV · Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate… · the same entry in another collection · chain B against B, 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 6EBV · PDBe 6EBV · UniProt A0A0D6HHM8
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