Research workbench
1.5 a X-ray crystal structure of apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding a site: RNA construct with 3'-overhang
Analyse 1.5 a X-ray crystal structure of apramycin complex with RNA fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OE5
- Type
- RNA
- Length
- 33 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*CP*G)- 3'); RNA (5'…
- Ligands
- AM2, MG, SO4
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'-R(*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*CP*G)- 3') | rna | 16 | — | — |
| B | RNA (5'- R(*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*CP*C)-3') | rna | 17 | — | — |
Ligands and binding sites
- AM2 · Apramycin · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.50 | 0.74 | 23 | AM2, MG |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 76 hydrogen bonds · nucleic-nucleic
Compared structures
- 2OE5 · 1.5 A X-ray crystal structure of Apramycin complex with RNA fragment… · 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 2OE5 · PDBe 2OE5
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