MolNFT v1 · #141722 · protein
Crystal structure of pfkrs with inhibitor clado-6
5ZH3 · Lysine-tRNA ligase: “Crystal structure of pfkrs with inhibitor clado-6”. X-ray diffraction, 2 ligands (LYS, 9CF), 10 pockets (best druggability 0.84). MolNFT v1 #141722 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZH3
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-tRNA ligase
- EC
- 6.1.1.6
- UniProt
- W7JP72
- Ligands
- LYS, 9CF
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 469 | 32% helix, 27% strand | W7JP72 |
| B | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 474 | 31% helix, 26% strand | W7JP72 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- 9CF · (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.84 | 0.97 | 58 | empty |
| 2 | 966 | 0.79 | 0.81 | 92 | LYS, 9CF |
| 3 | 977 | 0.77 | 0.80 | 87 | LYS, 9CF |
| 4 | 157 | 0.73 | 0.91 | 32 | empty |
| 5 | 127 | 0.59 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4392 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 5ZH3 · CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-6 · 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 5ZH3 · PDBe 5ZH3 · UniProt W7JP72
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