Research workbench
Crystal structure of LbCas12a in complex with crRNA and 13nt target DNA
Analyse Crystal structure of LbCas12a in complex with crRNA and 13nt target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8Y07
- Type
- protein + DNA + RNA
- Length
- 2,560 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Lachnospiraceae bacterium ND2006; SYNTHETIC CONSTRUCT
- Molecule
- LbCas12a; RNA (33-mer); DNA (5'-D(P*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*…
- UniProt
- A0A5S8WF58
- Ligands
- LI
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.85 · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A | LbCas12a | protein | 1214 | 46% helix, 13% strand | A0A5S8WF58 |
| F, B | RNA (33-mer) | rna | 33 | — | — |
| G, C | DNA (5'-D(P*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3') | dna | 22 | — | — |
| H, D | DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- LI · Lithium ion · metal · 4 copies · chains E, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.86 | 0.87 | 96 | empty |
| 2 | 770 | 0.84 | 0.88 | 79 | empty |
| 3 | 606 | 0.83 | 0.88 | 54 | empty |
| 4 | 1059 | 0.81 | 0.82 | 94 | empty |
| 5 | 1040 | 0.77 | 0.79 | 71 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3243 Ų buried · 79 hydrogen bonds · protein-nucleic
- E–F · 3105 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–C · 1507 Ų buried · 25 hydrogen bonds · protein-nucleic
- E–G · 1372 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–A · 1277 Ų buried · 16 hydrogen bonds · protein-protein
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 A0A5S8WF58
- Elsewhere: RCSB PDB 8Y07 · PDBe 8Y07 · UniProt A0A5S8WF58
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