MolNFT v1 · #1653 · protein
Aspartyl-tRNA synthetase
1B8A · Protein (aspartyl-tRNA synthetase): “Aspartyl-tRNA synthetase”. X-ray diffraction, 2 ligands (ATP, MN), 8 pockets (best druggability 0.76). MolNFT v1 #1653 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1B8A
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (aspartyl-tRNA synthetase)
- EC
- 6.1.1.12
- UniProt
- Q52428
- Ligands
- ATP, MN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (aspartyl-tRNA synthetase) (EC 6.1.1.12) | protein | 438 | 33% helix, 29% strand | Q52428 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.76 | 0.82 | 68 | MN, ATP |
| 2 | 564 | 0.73 | 0.81 | 56 | MN, ATP |
| 3 | 455 | 0.68 | 0.80 | 63 | empty |
| 4 | 76 | 0.58 | 0.88 | 25 | empty |
| 5 | 100 | 0.50 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 4523 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
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 Q52428
- Elsewhere: RCSB PDB 1B8A · PDBe 1B8A · UniProt Q52428
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