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Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. significance for the evolution of tobamoviruses
Analyse Structure determination of cucumber green mottle mosaic virus by X-ray fiber… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CGM
- Type
- protein + RNA
- Length
- 163 residues
- Chains
- 2
- Method
- fiber diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*GP*AP*A)-3'); Cucumber green mottle mosaic virus
- UniProt
- P19521
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.73
Structure
fiber diffraction · 2 distinct chains · 38% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | RNA (5'-R(P*GP*AP*A)-3') | rna | 3 | — | — |
| E | Cucumber green mottle mosaic virus | protein | 160 | 38% helix, 1% strand | P19521 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.73 | 0.95 | 21 | empty |
| 2 | 90 | 0.53 | 0.84 | 20 | empty |
| 3 | 63 | 0.43 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- I–E · 485 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1CGM · Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction.… · the same entry in another collection · chain I against I, 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 P19521
- Elsewhere: RCSB PDB 1CGM · PDBe 1CGM · UniProt P19521
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