Research workbench
Cryoem structure of the LBCAS12A-crrna-ACRVA4 complex
Analyse Cryoem structure of the LBCAS12A-crrna-ACRVA4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMA
- Type
- protein + RNA
- Length
- 1,460 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACRVA1; CPF1; RNA
- UniProt
- A0A0U2APF4, A0A182DWE3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACRVA1 | protein | 115 | 30% helix, 16% strand | A0A0U2APF4 |
| B | CPF1 | protein | 1206 | 39% helix, 12% strand | A0A182DWE3 |
| G | RNA | rna | 25 | — | — |
| C | ACRVA1 | protein | 114 | 29% helix, 18% strand | A0A0U2APF4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, G, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.76 | 0.92 | 31 | MG |
| 2 | 657 | 0.66 | 0.76 | 64 | empty |
| 3 | 426 | 0.59 | 0.75 | 39 | empty |
| 4 | 315 | 0.59 | 0.77 | 43 | empty |
| 5 | 412 | 0.58 | 0.75 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–G · 3034 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–B · 1523 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 762 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 179 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NMA · CryoEM structure of the LbCas12a-crRNA-AcrVA4 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
- Every structure of UniProt A0A182DWE3
- Elsewhere: RCSB PDB 6NMA · PDBe 6NMA · UniProt A0A0U2APF4 · UniProt A0A182DWE3
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