Research workbench
The structure of a pfi riboswitch bound to zmp
Analyse The structure of a pfi riboswitch bound to zmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZNP
- Type
- RNA
- Length
- 139 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfi riboswitch
- Ligands
- AMZ, MG
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfi riboswitch | rna | 73 | — | — |
| B | Pfi riboswitch | rna | 66 | — | — |
Ligands and binding sites
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.63 | 0.79 | 25 | empty |
| 2 | 345 | 0.60 | 0.78 | 24 | MG |
| 3 | 88 | 0.37 | 0.77 | 13 | AMZ |
| 4 | 144 | 0.36 | 0.73 | 16 | empty |
| 5 | 89 | 0.35 | 0.76 | 15 | AMZ |
Interfaces
1 interface between chains.
- A–B · 275 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 4ZNP · The structure of A pfI Riboswitch Bound to ZMP · 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 4ZNP · PDBe 4ZNP
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