MolNFT v2 · #225495 · protein + DNA + RNA
Crystal structure of LbCas12a in complex with crRNA and 13nt target DNA
8Y07: “Crystal structure of LbCas12a in complex with crRNA and 13nt target DNA”. X-ray diffraction at 2.85, 1 ligand (LI), 20 pockets (best druggability 0.86). MolNFT v2 #225495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.