MolNFT v1 · #175818 · protein + DNA + RNA
Crystal structure of the CAS12I1 R-loop complex before target DNA cleavage
7D2L · 12I1-D647A: “Crystal structure of the CAS12I1 R-loop complex before target DNA cleavage”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #175818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D2L
- Type
- protein + DNA + RNA
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12I1-D647A; RNA (43-mer); DNA (30-mer); DNA (26-mer)
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12I1-D647A | protein | 1077 | 50% helix, 14% strand | — |
| B | RNA (43-mer) | rna | 43 | — | — |
| C | DNA (30-mer) | dna | 30 | — | — |
| D | DNA (26-mer) | dna | 26 | — | — |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.79 | 0.81 | 70 | empty |
| 2 | 933 | 0.79 | 0.81 | 83 | empty |
| 3 | 489 | 0.75 | 0.84 | 42 | empty |
| 4 | 331 | 0.70 | 0.83 | 35 | empty |
| 5 | 301 | 0.69 | 0.84 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4122 Ų buried · 82 hydrogen bonds · protein-nucleic
- A–C · 2005 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 1805 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–C · 890 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- C–D · 485 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 7D2L · Crystal structure of the Cas12i1 R-loop complex before target DNA cleavage · the same entry in another collection · chain C against C, 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 7D2L · PDBe 7D2L
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