Research workbench
Crystal structure of rice dwarf virus P5 in complex with S- adenosylmethionine
Analyse Crystal structure of rice dwarf virus P5 in complex with S- adenosylmethionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6Y
- Type
- protein
- Length
- 2,960 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
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | — |
| B | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 694 | 40% helix, 18% strand | — |
| C | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 774 | 41% helix, 18% strand | — |
| D | MRNA capping enzyme P5 (EC 2.7.7.50) | protein | 713 | 41% helix, 19% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 3 copies · chains A, B, D
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 | 116 | 0.79 | 0.98 | 40 | empty |
| 2 | 852 | 0.78 | 0.81 | 44 | empty |
| 3 | 870 | 0.77 | 0.80 | 41 | empty |
| 4 | 96 | 0.77 | 0.98 | 19 | empty |
| 5 | 90 | 0.77 | 0.98 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2944 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2660 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X6Y · Crystal structure of Rice Dwarf Virus P5 in complex with S-adenosylmethionine · the same entry in another collection · chain B against B, 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 5X6Y · PDBe 5X6Y
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.