Research workbench
Fusobacterium ulcerans ztp riboswitch bound to zmp
Analyse Fusobacterium ulcerans ztp 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
- 5BTP
- Type
- RNA
- Length
- 124 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (62-mer)
- Ligands
- AMZ, MG, K
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (62-mer) | rna | 62 | — | — |
| A | RNA (62-mer) | rna | 62 | — | — |
Ligands and binding sites
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 12 copies · chains B, A
- K · Potassium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.68 | 0.80 | 30 | MG, AMZ |
| 2 | 513 | 0.68 | 0.79 | 30 | MG, AMZ, K |
| 3 | 137 | 0.37 | 0.73 | 15 | MG |
Interfaces
1 interface between chains.
- B–A · 585 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 5BTP · Fusobacterium ulcerans ZTP riboswitch bound to ZMP · the same entry in another collection · chain B against B, 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 5BTP · PDBe 5BTP
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