Research workbench
Structure of a C-di-gmp-II riboswitch from C. acetobutylicum bound to C-di-gmp
Analyse Structure of a C-di-gmp-II riboswitch from C. acetobutylicum bound to C-di-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q3Z
- Type
- RNA
- Length
- 150 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-di-gmp-II riboswitch
- Ligands
- C2E, MG
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V, A | C-di-gmp-II riboswitch | rna | 75 | — | — |
Ligands and binding sites
- 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 · 4 copies · chains V, A
- MG · Magnesium ion · metal · 13 copies · chains V, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.56 | 0.79 | 17 | MG |
| 2 | 209 | 0.51 | 0.78 | 24 | C2E, MG |
| 3 | 227 | 0.47 | 0.75 | 17 | MG |
| 4 | 217 | 0.42 | 0.73 | 16 | empty |
| 5 | 208 | 0.42 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- V–A · 398 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3Q3Z · Structure of a c-di-GMP-II riboswitch from C. acetobutylicum bound to c-di-GMP · the same entry in another collection · chain V against V, 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 3Q3Z · PDBe 3Q3Z
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