Research workbench
Molecular recognition of RNA by neomycin and a restricted neomycin derivative
Analyse Molecular recognition of RNA by neomycin and a restricted neomycin derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZX7
- Type
- RNA
- Length
- 116 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'…
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | 5'- R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3' | rna | 15 | — | — |
| B, D, F, H | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)- 3' | rna | 14 | — | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.54 | 0.73 | 28 | empty |
| 2 | 387 | 0.51 | 0.73 | 27 | empty |
| 3 | 372 | 0.50 | 0.73 | 24 | empty |
| 4 | 361 | 0.50 | 0.72 | 23 | empty |
| 5 | 58 | 0.28 | 0.75 | 10 | empty |
Interfaces
19 interfaces between chains.
- E–F · 712 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- C–D · 707 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- G–H · 696 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–B · 691 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- E–G · 101 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 1ZX7 · Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative · 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 1ZX7 · PDBe 1ZX7
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