MolNFT v1 · #157479 · protein
TRNA LIGASE
6N0T: “TRNA LIGASE”. X-ray diffraction, 3 ligands (ATP, MN, SO4), 4 pockets (best druggability 0.65). MolNFT v1 #157479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N0T
- Type
- protein
- Length
- 383 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA ligase
- EC
- 6.5.1.3
- UniProt
- G0S6G2
- Ligands
- ATP, MN, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA ligase (EC 6.5.1.3) | protein | 383 | 36% helix, 25% strand | G0S6G2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.65 | 0.80 | 35 | SO4, ATP, MN |
| 2 | 250 | 0.57 | 0.78 | 30 | empty |
| 3 | 211 | 0.56 | 0.79 | 27 | empty |
| 4 | 85 | 0.38 | 0.77 | 18 | empty |
Compared structures
- 6N0T · tRNA ligase · the same entry in another collection · chain A against A, 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 G0S6G2
- Elsewhere: RCSB PDB 6N0T · PDBe 6N0T · UniProt G0S6G2
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