Research workbench
Transition state structure of CPF1(CAS12A) I1 conformation
Analyse Transition state structure of CPF1(CAS12A) I1 conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GTC
- Type
- protein + DNA + RNA
- Length
- 1,345 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS12A; RNA (28-mer); DNA (5'…
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 30% helix, 10% 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 | 30% helix, 10% strand | A0Q7Q2 |
| B | RNA (28-mer) | rna | 28 | — | — |
| C | DNA (5'- D(P*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*AP*AP*CP*AP*AP*GP*CP*TP*CP*G)-3') | dna | 20 | — | — |
| 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 | 966 | 0.84 | 0.86 | 109 | empty |
| 2 | 908 | 0.81 | 0.83 | 82 | empty |
| 3 | 613 | 0.65 | 0.76 | 56 | empty |
| 4 | 336 | 0.61 | 0.78 | 28 | empty |
| 5 | 362 | 0.61 | 0.77 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3268 Ų buried · 70 hydrogen bonds · protein-nucleic
- A–C · 1480 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 955 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 595 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- B–C · 362 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GTC · Transition state structure of Cpf1(Cas12a) I1 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 0.75
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 6GTC · PDBe 6GTC · UniProt A0Q7Q2
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