MolNFT v1 · #151905 · protein + DNA + RNA
Crystal structure of catalytically inactive FNCAS12A in complex with a crrna guide and a dsdna target
6I1K · CRISPR-associated endonuclease CAS12A: “Crystal structure of catalytically inactive FNCAS12A in complex with a crrna guide and a dsdna target”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.80). MolNFT v1 #151905…
- PDB
- 6I1K
- Type
- protein + DNA + RNA
- Length
- 1,392 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS12A; Crrna (40-mer); DNA target strand (38-mer); DNA…
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1282 | 46% helix, 12% strand | A0Q7Q2 |
| B | Crrna (40-mer) | rna | 39 | — | — |
| C | DNA target strand (38-mer) | dna | 38 | — | — |
| D | DNA non-target strand (33-mer) | dna | 33 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1146 | 0.80 | 0.82 | 87 | MG, EDO |
| 2 | 511 | 0.76 | 0.84 | 59 | MG |
| 3 | 644 | 0.74 | 0.81 | 62 | empty |
| 4 | 564 | 0.69 | 0.79 | 44 | empty |
| 5 | 632 | 0.68 | 0.77 | 45 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 3821 Ų buried · 97 hydrogen bonds · protein-nucleic
- A–C · 2190 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–D · 1768 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 876 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–D · 768 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 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 0.95
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 6I1K · PDBe 6I1K · UniProt A0Q7Q2
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