MolNFT v1 · #77622 · RNA
Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine
3RKF: “Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine”. X-ray diffraction, 2 ligands (NCO, DX4), 12 pockets (best druggability 0.82). MolNFT v1 #77622 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RKF
- Type
- RNA
- Length
- 268 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine riboswitch
- Ligands
- NCO, DX4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Guanine riboswitch | rna | 67 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 26 copies · chains A, B, C, D
- DX4 · 2-amino-1,9-dihydro-6H-purine-6-thione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.82 | 0.84 | 66 | NCO |
| 2 | 639 | 0.72 | 0.81 | 36 | NCO |
| 3 | 564 | 0.70 | 0.80 | 36 | NCO |
| 4 | 285 | 0.65 | 0.83 | 25 | NCO |
| 5 | 282 | 0.64 | 0.82 | 29 | NCO |
Interfaces
6 interfaces between chains.
- A–B · 368 Ų buried · 1 hydrogen bond · nucleic-nucleic
- C–D · 368 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–C · 231 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- B–D · 113 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–C · 104 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 3RKF · Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine · 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 3RKF · PDBe 3RKF
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