MolNFT v1 · #152933 · protein
Crystal structure of human cytosolic aspartyl-tRNA synthetase (drs) in complex with glutathion-S transferase (GST) domains from aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (eprs)
6IY6 · Aspartate--tRNA ligase, cytoplasmic: “Crystal structure of human cytosolic aspartyl-tRNA synthetase (drs) in complex with glutathion-S transferase…”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.75).…
- PDB
- 6IY6
- Type
- protein
- Length
- 3,071 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--tRNA ligase, cytoplasmic; Aminoacyl tRNA synthase complex-interacting…
- EC
- 6.1.1.12, 6.1.1.17, 6.1.1.15
- UniProt
- P14868, Q13155, P07814
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12) | protein | 421 | 33% helix, 28% strand | P14868 |
| B | Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12) | protein | 419 | 34% helix, 28% strand | P14868 |
| C, D, I | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 192 | 46% helix, 14% strand | Q13155 |
| E, F, K, L | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 157 | 53% helix, 11% strand | P07814 |
| G, H | Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12) | protein | 417 | 34% helix, 27% strand | P14868 |
| J | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 193 | 46% helix, 13% strand | Q13155 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, G, H
- PO4 · Phosphate ion · ion · 17 copies · chains A, C, B, D, H, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.75 | 0.79 | 98 | PO4 |
| 2 | 223 | 0.73 | 0.88 | 24 | empty |
| 3 | 214 | 0.72 | 0.88 | 24 | empty |
| 4 | 200 | 0.71 | 0.88 | 22 | empty |
| 5 | 218 | 0.69 | 0.86 | 24 | empty |
Interfaces
21 interfaces between chains.
- A–B · 4520 Ų buried · 83 hydrogen bonds · protein-protein
- G–H · 4463 Ų buried · 82 hydrogen bonds · protein-protein
- C–E · 1153 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 1127 Ų buried · 12 hydrogen bonds · protein-protein
- J–L · 1124 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6IY6 · Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with… · the same entry in another collection · chain L against L, 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 P14868
- Every structure of UniProt Q13155
- Every structure of UniProt P07814
- Elsewhere: RCSB PDB 6IY6 · PDBe 6IY6 · UniProt P14868 · UniProt Q13155 · UniProt P07814
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