Research workbench
Cryo-EM structure of LBCAS12A-crrna: ACRVA4 (1:2 complex)
Analyse Cryo-EM structure of LBCAS12A-crrna: ACRVA4 (1:2 complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7M
- Type
- protein + RNA
- Length
- 1,193 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS12A; Mature crrna; Anti-CRISPR VA4
- UniProt
- A0A0U2APF4
- Ligands
- MG
- Pockets
- 15 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS12A | protein | 1070 | 43% helix, 12% strand | — |
| B | Mature crrna | rna | 25 | — | — |
| C | Anti-CRISPR VA4 | protein | 98 | 20% helix, 31% strand | A0A0U2APF4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.79 | 0.89 | 45 | MG |
| 2 | 734 | 0.68 | 0.76 | 71 | empty |
| 3 | 325 | 0.61 | 0.78 | 41 | empty |
| 4 | 305 | 0.61 | 0.78 | 36 | empty |
| 5 | 200 | 0.58 | 0.81 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2927 Ų buried · 60 hydrogen bonds · protein-nucleic
- A–C · 1588 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6P7M · Cryo-EM structure of LbCas12a-crRNA: AcrVA4 (1:2 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 6P7M · PDBe 6P7M · UniProt A0A0U2APF4
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