Research workbench
Cryoem structure of the LBCAS12A-crrna-ACRVA4 dimer
Analyse Cryoem structure of the LBCAS12A-crrna-ACRVA4 dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NM9
- Type
- protein + RNA
- Length
- 2,690 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACRVA4; CPF1; RNA (25-mer)
- UniProt
- A0A0U2APF4, A0A182DWE3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ACRVA4 | protein | 115 | 24% helix, 10% strand | A0A0U2APF4 |
| B, D | CPF1 | protein | 1205 | 41% helix, 11% strand | A0A182DWE3 |
| G, E | RNA (25-mer) | rna | 25 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, G, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.81 | 0.85 | 104 | MG |
| 2 | 187 | 0.74 | 0.91 | 24 | MG |
| 3 | 73 | 0.71 | 0.95 | 20 | empty |
| 4 | 749 | 0.69 | 0.76 | 75 | empty |
| 5 | 688 | 0.68 | 0.76 | 74 | empty |
Interfaces
10 interfaces between chains.
- B–G · 2975 Ų buried · 61 hydrogen bonds · protein-nucleic
- D–E · 2975 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–B · 1485 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1484 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 687 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NM9 · CryoEM structure of the LbCas12a-crRNA-AcrVA4 dimer · 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
- Every structure of UniProt A0A182DWE3
- Elsewhere: RCSB PDB 6NM9 · PDBe 6NM9 · UniProt A0A0U2APF4 · UniProt A0A182DWE3
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