Research workbench
Crystal structure of the capping enzyme P5 from rice dwarf virus
Analyse Crystal structure of the capping enzyme P5 from rice dwarf virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6X
- Type
- protein
- Length
- 3,111 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA capping enzyme P5
- EC
- 2.7.7.50
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 779 | 40% helix, 19% strand | — |
| A | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 776 | 40% helix, 19% strand | — |
| B | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 778 | 42% helix, 19% strand | — |
| D | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 778 | 41% helix, 19% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 22 | empty |
| 2 | 810 | 0.78 | 0.82 | 43 | empty |
| 3 | 873 | 0.78 | 0.81 | 95 | empty |
| 4 | 92 | 0.78 | 0.99 | 22 | empty |
| 5 | 777 | 0.77 | 0.82 | 44 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2990 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2940 Ų buried · 48 hydrogen bonds · protein-protein
- C–A · 573 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 348 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X6X · Crystal structure of the capping enzyme P5 from Rice Dwarf Virus · 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
- Elsewhere: RCSB PDB 5X6X · PDBe 5X6X
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