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Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of pseudorabies virus
Analyse Structural descriptions of ligand interactions to DNA and RNA quadruplexes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XRQ
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5' GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A-3')
- Ligands
- V8A, K
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | RNA (5' GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A-3') | rna | 14 | — | — |
Ligands and binding sites
- V8A · 2,7-bis[3-(morpholin-4-yl)propyl]-4,9-bis{[3-(morpholin-4-yl)propyl]amino}benzo[lmn][3, 8]phenanthroline-1,3,6,8(2H,7H)-tetrone · ligand · 2 copies · chains B, A
- K · Potassium ion · metal · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.31 | 0.76 | 8 | V8A |
| 2 | 52 | 0.30 | 0.77 | 10 | empty |
Interfaces
1 interface between chains.
- B–A · 478 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 6XRQ · Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from… · 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 6XRQ · PDBe 6XRQ
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