MolNFT v1 · #156114 · protein + DNA + RNA
Crystal structure of CAS12I2 ternary complex with single MG2+ bound in catalytic pocket
6LTR: “Crystal structure of CAS12I2 ternary complex with single MG2+ bound in catalytic pocket”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.78). MolNFT v1 #156114 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LTR
- Type
- protein + DNA + RNA
- Length
- 1,137 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*TP*T)-3'); DNA (35-mer)…
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS12I2 | protein | 1037 | 48% helix, 15% strand | — |
| B | RNA (56-mer) | rna | 49 | — | — |
| D | DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*TP*T)-3') | dna | 11 | — | — |
| C | DNA (35-mer) | dna | 35 | — | — |
| E | Trans ssdna | dna | 5 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.78 | 0.81 | 64 | empty |
| 2 | 663 | 0.75 | 0.81 | 59 | empty |
| 3 | 601 | 0.74 | 0.81 | 55 | empty |
| 4 | 699 | 0.73 | 0.80 | 50 | empty |
| 5 | 246 | 0.73 | 0.88 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4714 Ų buried · 136 hydrogen bonds · protein-nucleic
- A–C · 1896 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 1194 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–D · 938 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–E · 826 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 6LTR · Crystal structure of Cas12i2 ternary complex with single 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 6LTR · PDBe 6LTR
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