Research workbench
Cryo-EM structure of LbCas12a-crRNA: AcrVA4 (2:2 complex)
Analyse Cryo-EM structure of LbCas12a-crRNA: AcrVA4 (2:2 complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7N
- Type
- protein + RNA
- Length
- 2,402 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.9
- Source
- Lachnospiraceae bacterium ND2006; Moraxella bovoculi; SYNTHETIC CONSTRUCT
- Molecule
- anti-CRISPR VA4; Cas12a; mature crRNA
- UniProt
- A0A0U2APF4
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 4.9 · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | anti-CRISPR VA4 | protein | 106 | 26% helix, 28% strand | A0A0U2APF4 |
| A, E | Cas12a | protein | 1070 | 43% helix, 12% strand | — |
| B, F | mature crRNA | rna | 25 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.81 | 0.82 | 126 | empty |
| 2 | 123 | 0.76 | 0.96 | 19 | MG |
| 3 | 125 | 0.74 | 0.94 | 20 | MG |
| 4 | 831 | 0.70 | 0.76 | 73 | empty |
| 5 | 787 | 0.70 | 0.76 | 72 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2994 Ų buried · 58 hydrogen bonds · protein-nucleic
- E–F · 2992 Ų buried · 58 hydrogen bonds · protein-nucleic
- C–A · 1602 Ų buried · 17 hydrogen bonds · protein-protein
- G–E · 1555 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 374 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6P7N · Cryo-EM structure of LBCAS12A-crrna: ACRVA4 (2:2 complex) · the same entry in another collection · chain A against A, 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
- Every structure of UniProt A0A0U2APF4
- Elsewhere: RCSB PDB 6P7N · PDBe 6P7N · UniProt A0A0U2APF4
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