MolNFT v1 · #139199 · protein
The X-ray crystal structure of subunit fusion RNA splicing endonuclease from methanopyrus kandleri
5X89 · Enda-like PROTEIN,TRNA-splicing endonuclease: “The X-ray crystal structure of subunit fusion RNA splicing endonuclease from methanopyrus kandleri”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.38). MolNFT v1…
- PDB
- 5X89
- Type
- protein
- Length
- 337 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enda-like PROTEIN,TRNA-splicing endonuclease
- EC
- 4.6.1.16
- UniProt
- Q8TGZ5, Q8TGZ7
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enda-like PROTEIN,TRNA-splicing endonuclease (EC 4.6.1.16) | protein | 337 | 32% helix, 34% strand | Q8TGZ5, Q8TGZ7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.38 | 0.77 | 19 | empty |
| 2 | 67 | 0.37 | 0.77 | 13 | empty |
| 3 | 82 | 0.34 | 0.75 | 17 | empty |
Compared structures
- 5X89 · The X-ray crystal structure of subunit fusion RNA splicing endonuclease from Methanopyrus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TGZ7 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease (Q8TGZ7) · a predicted model of the same protein · chain A against A, TM-score 0.50
- Q8TGZ5 · AlphaFold monomer V2.0 prediction for enda-like protein (Q8TGZ5) · a predicted model of the same protein · chain A against A, TM-score 0.48
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 Q8TGZ5
- Every structure of UniProt Q8TGZ7
- Elsewhere: RCSB PDB 5X89 · PDBe 5X89 · UniProt Q8TGZ5 · UniProt Q8TGZ7
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