MolNFT v1 · #128636 · RNA
The structure of the thermobifida fusca guanidine III riboswitch with guanidine.
5NWQ: “The structure of the thermobifida fusca guanidine III riboswitch with guanidine.”. X-ray diffraction, 4 ligands (GAI, NA, MG), 4 pockets (best druggability 0.53). MolNFT v1 #128636 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NWQ
- Type
- RNA
- Length
- 82 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanidine III riboswitch
- Ligands
- GAI, NA, MG, K
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanidine III riboswitch | rna | 41 | — | — |
Ligands and binding sites
- GAI · Guanidine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.53 | 0.81 | 12 | GAI, NA |
| 2 | 140 | 0.45 | 0.78 | 12 | GAI, K, NA |
| 3 | 83 | 0.28 | 0.72 | 12 | empty |
| 4 | 58 | 0.27 | 0.74 | 11 | empty |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5NWQ · The structure of the thermobifida fusca guanidine III riboswitch with guanidine. · 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 5NWQ · PDBe 5NWQ
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