Research workbench
Crystal structure of aspartyl-tRNA synthetase from mycobacterium smegmatis with bound aspartic acid
Analyse Crystal structure of aspartyl-tRNA synthetase from mycobacterium smegmatis with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O2D
- Type
- protein
- Length
- 1,095 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--tRNA ligase
- EC
- 6.1.1.12
- UniProt
- A0QWN3
- Ligands
- ASP
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--tRNA ligase (EC 6.1.1.12) | protein | 580 | 32% helix, 26% strand | A0QWN3 |
| B | Aspartate--tRNA ligase (EC 6.1.1.12) | protein | 515 | 30% helix, 26% strand | A0QWN3 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.80 | 0.97 | 35 | empty |
| 2 | 1058 | 0.78 | 0.80 | 99 | ASP |
| 3 | 684 | 0.72 | 0.79 | 57 | ASP, TRS |
| 4 | 60 | 0.72 | 0.98 | 22 | empty |
| 5 | 57 | 0.68 | 0.96 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4476 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 4O2D · Crystal structure of aspartyl-tRNA synthetase from Mycobacterium smegmatis with bound… · the same entry in another collection · chain B against B, TM-score 1.00
- A0QWN3 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP/ASN) ligase (A0QWN3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A0QWN3
- Elsewhere: RCSB PDB 4O2D · PDBe 4O2D · UniProt A0QWN3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.