MolNFT v1 · #142827 · protein
Crystal structure of pfkrs complexed with chromone inhibitor
6AGT · Lysine--tRNA ligase: “Crystal structure of pfkrs complexed with chromone inhibitor”. X-ray diffraction, 3 ligands (9X0, LYS, CO), 20 pockets (best druggability 0.85). MolNFT v1 #142827 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6AGT
- Type
- protein
- Length
- 1,985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- W7JP72
- Ligands
- 9X0, LYS, CO
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 495 | 34% helix, 25% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 506 | 34% helix, 25% strand | W7JP72 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 499 | 34% helix, 25% strand | W7JP72 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 34% helix, 26% strand | W7JP72 |
Ligands and binding sites
- 9X0 · N-(cyclohexylmethyl)-4-oxo-4H-1-benzopyran-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 5 copies · chains A, B, C, D
- FMT · Formic acid · additive · 5 copies · chains A, B, D, C
- MLA · Malonic acid · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.85 | 0.91 | 87 | FMT |
| 2 | 188 | 0.81 | 0.96 | 45 | FMT |
| 3 | 654 | 0.78 | 0.84 | 69 | 9X0, CO, LYS |
| 4 | 668 | 0.77 | 0.83 | 68 | 9X0, CO, LYS |
| 5 | 852 | 0.77 | 0.81 | 83 | 9X0, CO, LYS |
Interfaces
5 interfaces between chains.
- A–B · 4594 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 4462 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 259 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 99 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 64 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6AGT · Crystal structure of PfKRS complexed with chromone inhibitor · 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 W7JP72
- Elsewhere: RCSB PDB 6AGT · PDBe 6AGT · UniProt W7JP72
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