Research workbench
Transient state structure of CRISPR-Cpf1 (Cas12a) I5 conformation
Analyse Transient state structure of CRISPR-Cpf1 (Cas12a) I5 conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GTF
- Type
- protein + DNA + RNA
- Length
- 1,346 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.63
- Source
- Francisella tularensis subsp. novicida U112; SYNTHETIC CONSTRUCT
- Molecule
- CRISPR-associated endonuclease Cas12a; RNA (29-mer); DNA…
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.63 · 4 distinct chains · 28% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease Cas12a (EC 3.1.21.1, 3.1.27.2) | protein | 1280 | 28% helix, 7% strand | A0Q7Q2 |
| B | RNA (29-mer) | rna | 29 | — | — |
| C | DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*AP*AP*CP*AP*AP*GP*CP*TP*CP*G)-3') | dna | 21 | — | — |
| D | DNA (5'-D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*A)-3') | dna | 16 | — | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.82 | 0.84 | 113 | empty |
| 2 | 99 | 0.73 | 0.94 | 23 | empty |
| 3 | 557 | 0.70 | 0.80 | 80 | empty |
| 4 | 102 | 0.66 | 0.89 | 25 | empty |
| 5 | 125 | 0.58 | 0.84 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3330 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–C · 1381 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 1046 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 527 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- B–C · 422 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GTF · Transient state structure of CRISPR-CPF1 (CAS12A) I5 conformation · the same entry in another collection · chain A against A, TM-score 1.00
- A0Q7Q2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (A0Q7Q2) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 A0Q7Q2
- Elsewhere: RCSB PDB 6GTF · PDBe 6GTF · UniProt A0Q7Q2
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