MolNFT v1 · #151906 · protein + DNA + RNA
Crystal structure of FNCAS12A in complex with a crrna guide and ssdna target
6I1L · CRISPR-associated endonuclease CAS12A: “Crystal structure of FNCAS12A in complex with a crrna guide and ssdna target”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.79). MolNFT v1 #151906 on GenesisL1: 3D…
- PDB
- 6I1L
- Type
- protein + DNA + RNA
- Length
- 2,650 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS12A; Crrna (40-mer); Ssdna target strand
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1277 | 48% helix, 13% strand | A0Q7Q2 |
| B | Crrna (40-mer) | rna | 40 | — | — |
| C, F | Ssdna target strand | dna | 20 | — | — |
| D | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1254 | 46% helix, 13% strand | A0Q7Q2 |
| E | Crrna (40-mer) | rna | 39 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 12 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 9 copies · chains A, B, D, E
- CIT · Citric acid · additive · 11 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.79 | 0.82 | 76 | empty |
| 2 | 783 | 0.79 | 0.83 | 73 | empty |
| 3 | 460 | 0.79 | 0.87 | 64 | empty |
| 4 | 1184 | 0.77 | 0.79 | 77 | CIT, K |
| 5 | 688 | 0.76 | 0.82 | 72 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4018 Ų buried · 87 hydrogen bonds · protein-nucleic
- D–E · 3839 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–C · 1817 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 1765 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1740 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6I1L · Crystal structure of FnCas12a in complex with a crRNA guide and ssDNA target · the same entry in another collection · chain F against F, TM-score 1.00
- A0Q7Q2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (A0Q7Q2) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 6I1L · PDBe 6I1L · UniProt A0Q7Q2
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