MolNFT v1 · #150427 · protein + DNA + RNA
Transient state structure of CRISPR-CPF1 (CAS12A) I2 conformation
6GTD · CRISPR-associated endonuclease CAS12A: “Transient state structure of CRISPR-CPF1 (CAS12A) I2 conformation”. Electron microscopy, 17 pockets (best druggability 0.71). MolNFT v1 #150427 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6GTD
- Type
- protein + DNA + RNA
- Length
- 1,335 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
- 17 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 28% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1269 | 28% helix, 6% 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*GP*T)-3') | dna | 18 | — | — |
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.71 | 0.77 | 141 | empty |
| 2 | 244 | 0.71 | 0.87 | 29 | empty |
| 3 | 720 | 0.70 | 0.78 | 79 | empty |
| 4 | 654 | 0.61 | 0.73 | 80 | empty |
| 5 | 454 | 0.61 | 0.76 | 74 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1404 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–D · 667 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–C · 532 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 525 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–D · 470 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6GTD · Transient state structure of CRISPR-Cpf1 (Cas12a) I2 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 6GTD · PDBe 6GTD · UniProt A0Q7Q2
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