MolNFT v1 · #95795 · protein
Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex
4J15 · Aspartate--tRNA ligase, cytoplasmic: “Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex”. X-ray diffraction, 15 pockets (best druggability 0.69). MolNFT v1 #95795 on…
- PDB
- 4J15
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--tRNA ligase, cytoplasmic
- EC
- 6.1.1.12
- UniProt
- P14868
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12) | protein | 431 | 36% helix, 26% strand | P14868 |
| B | Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12) | protein | 430 | 35% helix, 26% strand | P14868 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.69 | 0.80 | 42 | empty |
| 2 | 169 | 0.68 | 0.88 | 24 | GOL |
| 3 | 101 | 0.66 | 0.90 | 22 | empty |
| 4 | 369 | 0.63 | 0.78 | 44 | empty |
| 5 | 360 | 0.63 | 0.78 | 61 | GOL |
Interfaces
1 interface between chains.
- A–B · 3989 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 4J15 · Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P14868 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase, cytoplasmic (P14868) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14868
- Elsewhere: RCSB PDB 4J15 · PDBe 4J15 · UniProt P14868
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