Research workbench
Crystal structure of rice dwarf virus P5 in complex with a ssrna oligomer
Analyse Crystal structure of rice dwarf virus P5 in complex with a ssrna oligomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X70
- Type
- protein + RNA
- Length
- 3,047 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA capping enzyme P5; RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')
- EC
- 2.7.7.50
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 779 | 41% helix, 19% strand | — |
| C | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 753 | 42% helix, 19% strand | — |
| D | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 730 | 39% helix, 18% strand | — |
| B | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 780 | 41% helix, 19% strand | — |
| E | RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3') | rna | 3 | — | — |
| G | RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3') | rna | 2 | — | — |
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 | 735 | 0.78 | 0.83 | 44 | empty |
| 2 | 744 | 0.77 | 0.82 | 43 | empty |
| 3 | 978 | 0.77 | 0.79 | 85 | empty |
| 4 | 940 | 0.77 | 0.79 | 79 | empty |
| 5 | 81 | 0.75 | 0.98 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2978 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2934 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 397 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–B · 292 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5X70 · Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer · 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 5X70 · PDBe 5X70
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