MolNFT v1 · #5723 · protein
Crystal structure of free aspartyl-tRNA synthetase from escherichia COLI
1EQR: “Crystal structure of free aspartyl-tRNA synthetase from escherichia COLI”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.79). MolNFT v1 #5723 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EQR
- Type
- protein
- Length
- 1,770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl-tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- P21889
- Ligands
- MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 590 | 33% helix, 26% strand | P21889 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.79 | 0.97 | 26 | empty |
| 2 | 700 | 0.77 | 0.82 | 60 | empty |
| 3 | 748 | 0.77 | 0.81 | 87 | MG |
| 4 | 831 | 0.75 | 0.79 | 71 | MG |
| 5 | 719 | 0.75 | 0.80 | 65 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5320 Ų buried · 83 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 219 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1EQR · Crystal structure of free aspartyl-tRNA synthetase from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
- P21889 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase (P21889) · 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 P21889
- Elsewhere: RCSB PDB 1EQR · PDBe 1EQR · UniProt P21889
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