Research workbench
Crystal structure of an RNA aptamer in complex with Fab
Analyse Crystal structure of an RNA aptamer in complex with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KZE
- 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
- K, MG
- Pockets
- 9 · best druggability 0.66
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 | 11% helix, 49% strand | — |
| L | BL3-6 Fab antibody, light chain | protein | 215 | 6% helix, 51% strand | — |
| R | RNA (84-mer) | rna | 84 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.66 | 0.77 | 40 | MG |
| 2 | 339 | 0.65 | 0.80 | 41 | empty |
| 3 | 388 | 0.55 | 0.75 | 24 | empty |
| 4 | 315 | 0.53 | 0.74 | 34 | empty |
| 5 | 326 | 0.48 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2030 Ų buried · 19 hydrogen bonds · protein-protein
- H–R · 708 Ų buried · 15 hydrogen bonds · protein-nucleic
- L–R · 143 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 4KZE · Crystal structure of an RNA aptamer in complex with 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 4KZE · PDBe 4KZE
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