MolNFT v1 · #157481 · protein
TRNA LIGASE
6N0V: “TRNA LIGASE”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.78). MolNFT v1 #157481 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N0V
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA ligase
- EC
- 6.5.1.3
- UniProt
- G0S6G2
- Ligands
- MN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA ligase (EC 6.5.1.3) | protein | 395 | 34% helix, 24% strand | G0S6G2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.78 | 0.80 | 110 | empty |
| 2 | 257 | 0.60 | 0.79 | 27 | empty |
| 3 | 341 | 0.59 | 0.76 | 34 | empty |
| 4 | 272 | 0.56 | 0.77 | 35 | empty |
| 5 | 230 | 0.54 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6N0V · 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 6N0V · PDBe 6N0V · UniProt G0S6G2
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