Research workbench
Crystal structure of spinach RNA aptamer in complex with Fab BL3-6S97N
Analyse Crystal structure of spinach RNA aptamer in complex with Fab BL3-6S97N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B14
- Type
- protein + RNA
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab BL3-6S97N; Light chain of Fab BL3-6S97N; RNA (86-mer)
- Ligands
- MG
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab BL3-6S97N | protein | 225 | 8% helix, 49% strand | — |
| L | Light chain of Fab BL3-6S97N | protein | 215 | 5% helix, 51% strand | — |
| R | RNA (86-mer) | rna | 83 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.68 | 0.77 | 45 | MG |
| 2 | 263 | 0.62 | 0.81 | 37 | empty |
| 3 | 519 | 0.61 | 0.74 | 56 | empty |
| 4 | 378 | 0.56 | 0.75 | 25 | empty |
| 5 | 53 | 0.45 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2007 Ų buried · 15 hydrogen bonds · protein-protein
- H–R · 710 Ų buried · 17 hydrogen bonds · protein-nucleic
- L–R · 149 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6B14 · Crystal structure of Spinach RNA aptamer in complex with Fab BL3-6S97N · 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 6B14 · PDBe 6B14
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