Research workbench
Crystal structure of the SELENOMETHIONINE(SEMET)-derived CAS12I1 R- loop complex before target DNA cleavage
Analyse Crystal structure of the SELENOMETHIONINE(SEMET)-derived CAS12I1 R- loop… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EU9
- Type
- protein + DNA + RNA
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS12I1 D647A mutant; RNA (43-mer); DNA (31-mer); DNA (24-mer)
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS12I1 D647A mutant | protein | 1078 | 51% helix, 15% strand | — |
| B | RNA (43-mer) | rna | 43 | — | — |
| C | DNA (31-mer) | dna | 31 | — | — |
| D | DNA (24-mer) | dna | 24 | — | — |
Ligands and binding sites
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.79 | 0.93 | 22 | empty |
| 2 | 682 | 0.78 | 0.83 | 56 | empty |
| 3 | 325 | 0.70 | 0.84 | 41 | empty |
| 4 | 257 | 0.67 | 0.84 | 29 | empty |
| 5 | 715 | 0.67 | 0.76 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4275 Ų buried · 97 hydrogen bonds · protein-nucleic
- A–C · 2139 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 1978 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–C · 895 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- C–D · 474 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 7EU9 · Crystal structure of the selenomethionine(SeMet)-derived Cas12i1 R-loop complex before… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7EU9 · PDBe 7EU9
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