Research workbench
Cryo-EM structure of the CAS12F1-sgrna-target DNA complex
Analyse Cryo-EM structure of the CAS12F1-sgrna-target DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C7L
- Type
- protein + DNA + RNA
- Length
- 1,032 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated protein CAS14A.1; Sgrna; DNA (40-mer)
- UniProt
- A0A482D308
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated protein CAS14A.1 | protein | 503 | 42% helix, 18% strand | A0A482D308 |
| B | CRISPR-associated protein CAS14A.1 | protein | 372 | 41% helix, 17% strand | A0A482D308 |
| C | Sgrna | rna | 116 | — | — |
| D | DNA (40-mer) | dna | 27 | — | — |
| E | DNA (40-mer) | dna | 14 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.75 | 0.84 | 31 | empty |
| 2 | 464 | 0.75 | 0.84 | 48 | empty |
| 3 | 640 | 0.72 | 0.80 | 72 | empty |
| 4 | 156 | 0.70 | 0.90 | 22 | empty |
| 5 | 222 | 0.70 | 0.87 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3888 Ų buried · 90 hydrogen bonds · protein-nucleic
- B–C · 2040 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 1181 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1150 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–E · 1014 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 7C7L · Cryo-EM structure of the Cas12f1-sgRNA-target DNA 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 A0A482D308
- Elsewhere: RCSB PDB 7C7L · PDBe 7C7L · UniProt A0A482D308
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