Research workbench
Crystal structure of physalis mottle virus with intact ordered RNA
Analyse Crystal structure of physalis mottle virus with intact ordered RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XPJ
- Type
- protein + RNA
- Length
- 533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; 5'-R(CP*CP*CP)-3'
- UniProt
- P36351
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein | protein | 165 | 10% helix, 42% strand | P36351 |
| B | Coat protein | protein | 180 | 10% helix, 45% strand | P36351 |
| C | Coat protein | protein | 185 | 10% helix, 42% strand | P36351 |
| D | 5'-R(CP*CP*CP)-3' | rna | 3 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.53 | 0.77 | 32 | empty |
| 2 | 85 | 0.42 | 0.79 | 25 | empty |
| 3 | 56 | 0.28 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 995 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 739 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 699 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 244 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2XPJ · Crystal structure of Physalis Mottle Virus with intact ordered RNA · 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 P36351
- Elsewhere: RCSB PDB 2XPJ · PDBe 2XPJ · UniProt P36351
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.