Research workbench
A-site RNA in complex with neamine
Analyse A-site RNA in complex with neamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4S
- Type
- RNA
- Length
- 42 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*U P*CP*GP*C)-3'
- Ligands
- XXX
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*U P*CP*GP*C)-3' | rna | 21 | — | — |
Ligands and binding sites
- XXX · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2, 6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · chains A, B
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 | 312 | 0.48 | 0.73 | 21 | empty |
| 2 | 91 | 0.30 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 99 hydrogen bonds · nucleic-nucleic
Compared structures
- 2F4S · A-site RNA in complex with neamine · 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
- Elsewhere: RCSB PDB 2F4S · PDBe 2F4S
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