Research workbench
Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch
Analyse Crystal structure of an in vitro evolved tetracycline aptamer and artificial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EGZ
- Type
- protein + RNA
- Length
- 156 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; Tetracycline aptamer and artificial riboswitch
- UniProt
- P09012
- Ligands
- CTC, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U1 small nuclear ribonucleoprotein a | protein | 91 | 33% helix, 26% strand | P09012 |
| B | Tetracycline aptamer and artificial riboswitch | rna | 65 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.67 | 0.77 | 38 | MG |
| 2 | 257 | 0.49 | 0.75 | 20 | MG |
| 3 | 154 | 0.40 | 0.74 | 18 | MG |
| 4 | 84 | 0.34 | 0.75 | 12 | CTC, MG |
Interfaces
1 interface between chains.
- A–B · 974 Ų buried · 29 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3EGZ · Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch · 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
- Every structure of UniProt P09012
- Elsewhere: RCSB PDB 3EGZ · PDBe 3EGZ · UniProt P09012
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