Research workbench
Transient state structure of CRISPR-CPF1 (CAS12A) I3 conformation
Analyse Transient state structure of CRISPR-CPF1 (CAS12A) I3 conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GTE
- Type
- protein + DNA + RNA
- Length
- 1,341 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS12A; RNA (29-mer); DNA (5'…
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 30% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1274 | 30% helix, 8% 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*AP*G)-3') | dna | 17 | — | — |
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 | 217 | 0.78 | 0.92 | 34 | empty |
| 2 | 53 | 0.72 | 0.98 | 16 | empty |
| 3 | 797 | 0.70 | 0.77 | 85 | empty |
| 4 | 440 | 0.66 | 0.79 | 47 | empty |
| 5 | 337 | 0.66 | 0.81 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3218 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–C · 1564 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 1048 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 548 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- B–C · 421 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GTE · Transient state structure of CRISPR-Cpf1 (Cas12a) I3 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 6GTE · PDBe 6GTE · UniProt A0Q7Q2
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