Research workbench
Crystal structure of CAS12I2 ternary complex with double MG2+ bound in catalytic pocket
Analyse Crystal structure of CAS12I2 ternary complex with double MG2+ bound in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LTU
- Type
- protein + DNA + RNA
- Length
- 1,133 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS12I2; RNA (56-mer); DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3'); DNA (35-mer)…
- Ligands
- MG
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS12I2 | protein | 1034 | 49% helix, 15% strand | — |
| B | RNA (56-mer) | rna | 49 | — | — |
| D | DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3') | dna | 11 | — | — |
| C | DNA (35-mer) | dna | 35 | — | — |
| E | Trans ssdna | dna | 4 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.79 | 0.81 | 86 | empty |
| 2 | 824 | 0.76 | 0.81 | 65 | empty |
| 3 | 512 | 0.73 | 0.82 | 46 | MG |
| 4 | 72 | 0.72 | 0.97 | 22 | empty |
| 5 | 354 | 0.71 | 0.84 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4755 Ų buried · 146 hydrogen bonds · protein-nucleic
- A–C · 1917 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 1191 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- A–D · 925 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 687 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6LTU · Crystal structure of Cas12i2 ternary complex with double Mg2+ bound in catalytic pocket · 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 6LTU · PDBe 6LTU
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