MolNFT v1 · #33789 · protein
Crystal structure of tRNA-intron endonuclease from sulfolobus tokodaii
2CV8 · TRNA-splicing endonuclease: “Crystal structure of tRNA-intron endonuclease from sulfolobus tokodaii”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.54). MolNFT v1 #33789 on GenesisL1: 3D structure, binding sites…
- PDB
- 2CV8
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-splicing endonuclease
- EC
- 3.1.27.9
- UniProt
- Q975R3
- Ligands
- CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 160 | 32% helix, 35% strand | Q975R3 |
| B | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 180 | 34% helix, 32% strand | Q975R3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.54 | 0.78 | 24 | CL |
| 2 | 219 | 0.53 | 0.77 | 26 | CL |
Interfaces
1 interface between chains.
- A–B · 1404 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2CV8 · Crystal structure of tRNA-intron endonuclease from Sulfolobus tokodaii · the same entry in another collection · chain A against A, TM-score 1.00
- Q975R3 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease (Q975R3) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q975R3
- Elsewhere: RCSB PDB 2CV8 · PDBe 2CV8 · UniProt Q975R3
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