Research workbench
Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab
Analyse Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q9R
- Type
- protein + RNA
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab BL3-6, heavy chain; Fab BL3-6, light chain; Spinach RNA aptamer
- Ligands
- 2ZY, K
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab BL3-6, heavy chain | protein | 223 | 9% helix, 49% strand | — |
| L | Fab BL3-6, light chain | protein | 214 | 6% helix, 51% strand | — |
| R | Spinach RNA aptamer | rna | 84 | — | — |
Ligands and binding sites
- 2ZY · (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one · ligand · chains R
- K · Potassium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.73 | 0.78 | 59 | 2ZY |
| 2 | 494 | 0.60 | 0.74 | 49 | empty |
| 3 | 249 | 0.56 | 0.78 | 36 | empty |
| 4 | 383 | 0.55 | 0.75 | 24 | empty |
| 5 | 382 | 0.52 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1965 Ų buried · 14 hydrogen bonds · protein-protein
- H–R · 707 Ų buried · 14 hydrogen bonds · protein-nucleic
- L–R · 141 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 4Q9R · Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with… · the same entry in another collection · chain H against H, 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 4Q9R · PDBe 4Q9R
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