MolNFT v1 · #158182 · protein + RNA
Cryo-EM structure of the LBCAS12A-crrna-ACRVA1 complex
6NMD · CPF1: “Cryo-EM structure of the LBCAS12A-crrna-ACRVA1 complex”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #158182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NMD
- Type
- protein + RNA
- Length
- 1,383 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CPF1; Crrna; ACRVA1
- UniProt
- A0A182DWE3, A0A0U2BNN7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CPF1 | protein | 1202 | 42% helix, 9% strand | A0A182DWE3 |
| G | Crrna | rna | 25 | — | — |
| B | ACRVA1 | protein | 156 | 55% helix, 0% strand | A0A0U2BNN7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.83 | 0.85 | 95 | empty |
| 2 | 1149 | 0.78 | 0.80 | 79 | empty |
| 3 | 557 | 0.77 | 0.84 | 56 | empty |
| 4 | 658 | 0.68 | 0.77 | 60 | empty |
| 5 | 110 | 0.67 | 0.90 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–G · 2890 Ų buried · 65 hydrogen bonds · protein-nucleic
- A–B · 2075 Ų buried · 20 hydrogen bonds · protein-protein
- G–B · 310 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6NMD · cryo-EM Structure of the LbCas12a-crRNA-AcrVA1 complex · the same entry in another collection · chain B against B, 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 A0A182DWE3
- Every structure of UniProt A0A0U2BNN7
- Elsewhere: RCSB PDB 6NMD · PDBe 6NMD · UniProt A0A182DWE3 · UniProt A0A0U2BNN7
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