MolNFT v1 · #110918 · RNA
3',3'-cgamp riboswitch bound with C-di-gmp
4YB0 · RNA (84-mer): “3',3'-cgamp riboswitch bound with C-di-gmp”. X-ray diffraction, 4 ligands (GDP, C2E, MG), 7 pockets (best druggability 0.63). MolNFT v1 #110918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YB0
- Type
- RNA
- Length
- 166 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (84-mer)
- Ligands
- GDP, C2E, MG, K
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, A | RNA (84-mer) | rna | 83 | — | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains R, A
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains R, A
- MG · Magnesium ion · metal · 5 copies · chains R, A
- K · Potassium ion · metal · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.63 | 0.77 | 32 | MG |
| 2 | 411 | 0.62 | 0.78 | 31 | MG |
| 3 | 675 | 0.61 | 0.74 | 46 | K |
| 4 | 430 | 0.54 | 0.74 | 32 | empty |
| 5 | 149 | 0.47 | 0.78 | 16 | C2E |
Interfaces
1 interface between chains.
- R–A · 12 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4YB0 · 3',3'-cGAMP riboswitch bound with c-di-GMP · the same entry in another collection · chain R against R, 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 4YB0 · PDBe 4YB0
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