Research workbench
RNA octamer containing glycol nucleic acid, sgnt
Analyse RNA octamer containing glycol nucleic acid, sgnt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V2H
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
- Ligands
- ZTH, NCO, MG
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- ZTH · (S)-1'-(2',3'-dihydroxypropyl)-thymine · ligand · 4 copies · chains A, B, C, D
- NCO · Cobalt hexammine(iii) · ligand · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
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 | 130 | 0.33 | 0.72 | 17 | NCO, MG |
Interfaces
6 interfaces between chains.
- C–D · 414 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–B · 403 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–C · 108 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 102 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 39 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 8 covalent, 4 modified (covalent ligand, nucleotide modification).
Compared structures
- 5V2H · RNA octamer containing glycol nucleic acid, SgnT · 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 5V2H · PDBe 5V2H
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.