MolNFT v1 · #137881 · protein
Crystal structure of aspartyl-tRNA synthetase from mycobacterium tuberculosis complexed with L-aspartic acid
5W25 · Aspartate--TRNA(ASP/ASN) ligase: “Crystal structure of aspartyl-tRNA synthetase from mycobacterium tuberculosis complexed with L-aspartic acid”. X-ray diffraction, 3 ligands (LYS, ASP, GLU), 20 pockets (best druggability 0.77).…
- PDB
- 5W25
- Type
- protein
- Length
- 1,149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--TRNA(ASP/ASN) ligase
- EC
- 6.1.1.23
- UniProt
- P9WFW3
- Ligands
- LYS, ASP, GLU
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--TRNA(ASP/ASN) ligase (EC 6.1.1.23) | protein | 583 | 31% helix, 25% strand | P9WFW3 |
| B | Aspartate--TRNA(ASP/ASN) ligase (EC 6.1.1.23) | protein | 566 | 27% helix, 26% strand | P9WFW3 |
Ligands and binding sites
- LYS · Lysine · ligand · 3 copies · chains A, B
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.77 | 0.81 | 104 | ASP |
| 2 | 886 | 0.75 | 0.79 | 102 | ASP |
| 3 | 77 | 0.74 | 0.98 | 24 | empty |
| 4 | 353 | 0.73 | 0.85 | 40 | empty |
| 5 | 118 | 0.71 | 0.92 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 4446 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 5W25 · Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFW3 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP/ASN) ligase (P9WFW3) · a predicted model of the same protein · chain A 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 P9WFW3
- Elsewhere: RCSB PDB 5W25 · PDBe 5W25 · UniProt P9WFW3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.