MolNFT v1 · #141721 · protein
Crystal structure of pfkrs with inhibitor clado-5
5ZH2 · Lysine-tRNA ligase: “Crystal structure of pfkrs with inhibitor clado-5”. X-ray diffraction, 3 ligands (LYS, 9CU, CL), 12 pockets (best druggability 0.84). MolNFT v1 #141721 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZH2
- Type
- protein
- Length
- 939 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, 9CU, CL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 464 | 33% helix, 28% strand | W7JP72 |
| B | Lysine-tRNA ligase (EC 6.1.1.6) | protein | 475 | 33% helix, 27% strand | W7JP72 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- 9CU · (3R)-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
- CL · Chloride ion · ion · 4 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.84 | 0.96 | 53 | empty |
| 2 | 598 | 0.73 | 0.81 | 62 | LYS, 9CU |
| 3 | 291 | 0.72 | 0.85 | 33 | empty |
| 4 | 463 | 0.71 | 0.82 | 61 | LYS, 9CU, CL |
| 5 | 278 | 0.71 | 0.85 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 4553 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 5ZH2 · CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-5 · 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 5ZH2 · PDBe 5ZH2 · UniProt W7JP72
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