Research workbench
Crystal structure of the CAS12I1 R-loop complex after target DNA cleavage
Analyse Crystal structure of the CAS12I1 R-loop complex after target DNA cleavage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3J
- Type
- protein + DNA + RNA
- Length
- 1,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12I1-wt; RNA (43-mer); DNA (28-mer); DNA (23-mer)
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12I1-wt | protein | 1077 | 49% helix, 14% strand | — |
| B | RNA (43-mer) | rna | 43 | — | — |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (23-mer) | dna | 23 | — | — |
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 | 341 | 0.78 | 0.89 | 53 | empty |
| 2 | 558 | 0.69 | 0.79 | 39 | empty |
| 3 | 296 | 0.67 | 0.83 | 29 | empty |
| 4 | 636 | 0.66 | 0.76 | 31 | empty |
| 5 | 209 | 0.65 | 0.84 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4207 Ų buried · 88 hydrogen bonds · protein-nucleic
- A–C · 2038 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–D · 1271 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 870 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- C–D · 393 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 7D3J · Crystal structure of the Cas12i1 R-loop complex after target DNA cleavage · 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 7D3J · PDBe 7D3J
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.