MolNFT v1 · #158566 · protein + DNA + RNA
Casx-grna-DNA(45BP) state I
6NY2 · DNA target strand: “Casx-grna-DNA(45BP) state I”. Electron microscopy, 20 pockets (best druggability 0.74). MolNFT v1 #158566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NY2
- Type
- protein + DNA + RNA
- Length
- 1,095 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA target strand; DNA non-target strand; Casx; RNA (110-mer)
- UniProt
- A0A357BT59
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA target strand | dna | 35 | — | — |
| D | DNA non-target strand | dna | 35 | — | — |
| Y | Casx | protein | 915 | 36% helix, 9% strand | A0A357BT59 |
| B | RNA (110-mer) | rna | 110 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.74 | 0.77 | 87 | empty |
| 2 | 366 | 0.74 | 0.86 | 43 | empty |
| 3 | 560 | 0.73 | 0.81 | 32 | empty |
| 4 | 345 | 0.73 | 0.85 | 37 | empty |
| 5 | 690 | 0.71 | 0.79 | 56 | empty |
Interfaces
6 interfaces between chains.
- Y–B · 5016 Ų buried · 93 hydrogen bonds · protein-nucleic
- C–Y · 2264 Ų buried · 41 hydrogen bonds · protein-nucleic
- D–Y · 2010 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–B · 907 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- C–D · 707 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NY2 · CasX-gRNA-DNA(45bp) state I · 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
- Every structure of UniProt A0A357BT59
- Elsewhere: RCSB PDB 6NY2 · PDBe 6NY2 · UniProt A0A357BT59
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