MolNFT v1 · #26276 · protein
Isoleucyl-tRNA synthetase editing domain complexed with the pre-transfer editing substrate analogue, val-ams
1WK8: “Isoleucyl-tRNA synthetase editing domain complexed with the pre-transfer editing substrate analogue, val-ams”. X-ray diffraction, 1 ligand (VMS), 2 pockets (best druggability 0.41). MolNFT v1 #26276 on GenesisL1: 3D structure…
- PDB
- 1WK8
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoleucyl-tRNA synthetase
- EC
- 6.1.1.5
- UniProt
- P56690
- Ligands
- VMS
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoleucyl-tRNA synthetase (EC 6.1.1.5) | protein | 182 | 26% helix, 31% strand | P56690 |
| B | Isoleucyl-tRNA synthetase (EC 6.1.1.5) | protein | 187 | 25% helix, 30% strand | P56690 |
Ligands and binding sites
- VMS · 5'O-[N-(L-valyl)sulphamoyl]adenosine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.41 | 0.75 | 20 | empty |
| 2 | 110 | 0.39 | 0.75 | 21 | VMS |
Compared structures
- 1WK8 · Isoleucyl-tRNA synthetase editing domain complexed with the pre-transfer editing… · the same entry in another collection · chain A against A, TM-score 1.00
- P56690 · AlphaFold monomer V2.0 prediction for isoleucine--tRNA ligase (P56690) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P56690
- Elsewhere: RCSB PDB 1WK8 · PDBe 1WK8 · UniProt P56690
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