Research workbench
Pantothenamide-bound pantothenate kinase from staphylococcus aureus
Analyse Pantothenamide-bound pantothenate kinase from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NB4
- Type
- protein
- Length
- 2,113 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- Q6G7I0
- Ligands
- ADP, SH3, MG
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 43% helix, 24% strand | Q6G7I0 |
| B | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 43% helix, 24% strand | Q6G7I0 |
| C | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 43% helix, 24% strand | Q6G7I0 |
| D | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 44% helix, 23% strand | Q6G7I0 |
| E | Type II pantothenate kinase (EC 2.7.1.33) | protein | 259 | 43% helix, 24% strand | Q6G7I0 |
| F | Type II pantothenate kinase (EC 2.7.1.33) | protein | 262 | 44% helix, 21% strand | Q6G7I0 |
| G | Type II pantothenate kinase (EC 2.7.1.33) | protein | 265 | 43% helix, 24% strand | Q6G7I0 |
| H | Type II pantothenate kinase (EC 2.7.1.33) | protein | 267 | 42% helix, 25% strand | Q6G7I0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SH3 · N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.84 | 0.85 | 130 | ADP, SH3, MG |
| 2 | 781 | 0.84 | 0.87 | 98 | ADP, SH3, MG |
| 3 | 930 | 0.83 | 0.85 | 93 | SH3, ADP, MG |
| 4 | 894 | 0.83 | 0.85 | 106 | SH3, ADP, MG |
| 5 | 581 | 0.82 | 0.87 | 83 | ADP, SH3, MG |
Interfaces
13 interfaces between chains.
- A–B · 2251 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2226 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2193 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2193 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 456 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4NB4 · Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus · the same entry in another collection · chain H against H, TM-score 1.00
- Q6G7I0 · AlphaFold monomer V2.0 prediction for type II pantothenate kinase (Q6G7I0) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 Q6G7I0
- Elsewhere: RCSB PDB 4NB4 · PDBe 4NB4 · UniProt Q6G7I0
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