Research workbench
Crystal structure of an RNA aptamer in complex with fluorophore and Fab
Analyse Crystal structure of an RNA aptamer in complex with fluorophore and Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KZD
- Type
- protein + RNA
- Length
- 524 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BL3-6 Fab antibody, heavy chain; BL3-6 Fab antibody, light chain; RNA (84-mer)
- Ligands
- 1TU, GLC, FRU, K, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | BL3-6 Fab antibody, heavy chain | protein | 225 | 10% helix, 49% strand | — |
| L | BL3-6 Fab antibody, light chain | protein | 215 | 6% helix, 50% strand | — |
| R | RNA (84-mer) | rna | 84 | — | — |
Ligands and binding sites
- 1TU · 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol · ligand · chains R
- GLC · alpha-D-glucopyranose · sugar · chains H, L
- FRU · beta-D-fructofuranose · sugar · chains H, L
- K · Potassium ion · metal · chains R
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.71 | 0.78 | 52 | MG, 1TU |
| 2 | 242 | 0.62 | 0.81 | 40 | empty |
| 3 | 403 | 0.58 | 0.75 | 47 | empty |
| 4 | 391 | 0.55 | 0.74 | 24 | empty |
| 5 | 355 | 0.50 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2031 Ų buried · 18 hydrogen bonds · protein-protein
- H–R · 713 Ų buried · 18 hydrogen bonds · protein-nucleic
- L–R · 137 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 4KZD · Crystal structure of an RNA aptamer in complex with fluorophore and Fab · 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 4KZD · PDBe 4KZD
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