Research workbench
Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E
Analyse Crystal structure of the mutant I26A/N52A of the endoribonuclease from human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1T
- Type
- protein
- Length
- 2,052 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0C6X1
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 342 | 21% helix, 32% strand | P0C6X1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.76 | 0.85 | 73 | empty |
| 2 | 529 | 0.76 | 0.83 | 76 | empty |
| 3 | 529 | 0.75 | 0.83 | 66 | empty |
| 4 | 491 | 0.73 | 0.82 | 64 | empty |
| 5 | 213 | 0.71 | 0.88 | 52 | empty |
Interfaces
8 interfaces between chains.
- C–E · 1342 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1321 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1302 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1295 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1291 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4S1T · Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus… · 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 P0C6X1
- Elsewhere: RCSB PDB 4S1T · PDBe 4S1T · UniProt P0C6X1
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