Research workbench
Crystal structure of double-helical cgg-repetitive RNA 19MER complexed with rss P19
Analyse Crystal structure of double-helical cgg-repetitive RNA 19MER complexed with rss… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KQ0
- Type
- protein + RNA
- Length
- 282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA silencing suppressor P19; 5'-R(P*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*C…
- UniProt
- P69517
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA silencing suppressor P19 | protein | 122 | 39% helix, 26% strand | P69517 |
| B, E | 5'-R(P*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*C P*C)-3' | rna | 19 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.63 | 0.75 | 42 | SO4 |
| 2 | 581 | 0.62 | 0.75 | 45 | SO4 |
| 3 | 83 | 0.47 | 0.82 | 23 | empty |
| 4 | 97 | 0.45 | 0.80 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–E · 957 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- A–D · 852 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 527 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 527 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 407 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4KQ0 · Crystal structure of double-helical CGG-repetitive RNA 19mer complexed with RSS p19 · 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 P69517
- Elsewhere: RCSB PDB 4KQ0 · PDBe 4KQ0 · UniProt P69517
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