MolNFT v1 · #30287 · RNA
Molecular recognition of RNA by neomycin and a restricted neomycin derivative
1ZZ5 · 5'- R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3': “Molecular recognition of RNA by neomycin and a restricted neomycin derivative”. X-ray diffraction, 2 ligands (CNY, MG), 2 pockets (best druggability 0.36). MolNFT v1 #30287 on…
- PDB
- 1ZZ5
- Type
- RNA
- Length
- 58 nucleotides
- Chains
- 4
- 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'…
- Ligands
- CNY, MG
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'- R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3' | rna | 15 | — | — |
| B, D | 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)- 3' | rna | 14 | — | — |
Ligands and binding sites
- CNY · 13,15-diamino-2-(aminomethyl)-3,4,9,12-tetrahydroxyhexadecahydro-2H-7,10-epoxypyrano[2,3-b][1,10,4]benzodioxazacyclododecin-8-yl 2,6-diamino-2,6-dideoxyhexopyranoside · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies
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 | 137 | 0.36 | 0.72 | 14 | MG |
| 2 | 121 | 0.34 | 0.73 | 13 | MG |
Interfaces
5 interfaces between chains.
- A–B · 705 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- C–D · 705 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–C · 118 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- B–D · 74 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–C · 51 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 1ZZ5 · 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 1ZZ5 · PDBe 1ZZ5
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