MolNFT v1 · #110917 · RNA
3',3'-cgamp riboswitch bound with 3',3'-cgamp
4YAZ · RNA (84-mer): “3',3'-cgamp riboswitch bound with 3',3'-cgamp”. X-ray diffraction, 3 ligands (4BW, MG, K), 9 pockets (best druggability 0.59). MolNFT v1 #110917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YAZ
- Type
- RNA
- Length
- 168 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (84-mer)
- Ligands
- 4BW, MG, K
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, A | RNA (84-mer) | rna | 84 | — | — |
Ligands and binding sites
- 4BW · 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9, 2,8]tetraoxadiphosphacyclododecin-2-yl]-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 · 3 copies · chains R, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.59 | 0.75 | 25 | MG |
| 2 | 501 | 0.58 | 0.74 | 30 | MG |
| 3 | 234 | 0.51 | 0.77 | 22 | empty |
| 4 | 216 | 0.48 | 0.76 | 19 | empty |
| 5 | 163 | 0.48 | 0.78 | 16 | 4BW |
Interfaces
1 interface between chains.
- R–A · 166 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4YAZ · 3',3'-cGAMP riboswitch bound with 3',3'-cGAMP · 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 4YAZ · PDBe 4YAZ
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