MolNFT v1 · #110056 · protein
Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from pseudomonas aeruginosa
4XKZ · Valine-tRNA ligase: “Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from pseudomonas…”. X-ray diffraction, 1 ligand (IOD), 2 pockets (best druggability 0.51). MolNFT v1 #110056 on…
- PDB
- 4XKZ
- Type
- protein
- Length
- 251 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Valine-tRNA ligase
- EC
- 6.1.1.9
- UniProt
- Q9HXH0
- Ligands
- IOD
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Valine-tRNA ligase (EC 6.1.1.9) | protein | 251 | 60% helix, 10% strand | Q9HXH0 |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.51 | 0.79 | 28 | IOD |
| 2 | 77 | 0.40 | 0.79 | 19 | empty |
Compared structures
- 4XKZ · Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HXH0 · AlphaFold monomer V2.0 prediction for valine--tRNA ligase (Q9HXH0) · 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 Q9HXH0
- Elsewhere: RCSB PDB 4XKZ · PDBe 4XKZ · UniProt Q9HXH0
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