Research workbench
5'-monophosphate Z:P guanine riboswitch bound to hypoxanthine.
Analyse 5'-monophosphate Z:P guanine riboswitch bound to hypoxanthine. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C7W
- Type
- RNA
- Length
- 65 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-monophosphate Z:P guanine riboswitch
- Ligands
- NCO, 50N, 50L, HPA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-monophosphate Z:P guanine riboswitch | rna | 65 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 8 copies · chains C
- 50N · (1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol · ligand · chains C
- 50L · [(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-1$L^{4},3,5, 7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains C
- HPA · Hypoxanthine · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.69 | 0.75 | 38 | NCO |
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5C7W · 5'-monophosphate Z:P Guanine Riboswitch bound to hypoxanthine. · the same entry in another collection · chain C against C, 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 5C7W · PDBe 5C7W
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