MolNFT v1 · #141724 · protein
Crystal structure of pfkrs with inhibitor clado-2
5ZH5 · Lysine--tRNA ligase: “Crystal structure of pfkrs with inhibitor clado-2”. X-ray diffraction, 3 ligands (LYS, 9CX, CL), 12 pockets (best druggability 0.85). MolNFT v1 #141724 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZH5
- Type
- protein
- Length
- 953 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, 9CX, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 482 | 31% helix, 26% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 471 | 33% helix, 25% strand | W7JP72 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- 9CX · (3S)-6,8-dihydroxy-3-{[(2R,6S)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.85 | 0.96 | 54 | empty |
| 2 | 972 | 0.79 | 0.81 | 96 | LYS, 9CX |
| 3 | 997 | 0.76 | 0.78 | 100 | LYS, 9CX |
| 4 | 133 | 0.58 | 0.84 | 28 | empty |
| 5 | 171 | 0.58 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 4342 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZH5 · CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-2 · 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 W7JP72
- Elsewhere: RCSB PDB 5ZH5 · PDBe 5ZH5 · UniProt W7JP72
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