MolNFT v1 · #158567 · protein + DNA + RNA
Casx ternary complex with 30BP target DNA
6NY3 · DNA target strand: “Casx ternary complex with 30BP target DNA”. Electron microscopy, 20 pockets (best druggability 0.74). MolNFT v1 #158567 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NY3
- Type
- protein + DNA + RNA
- Length
- 1,079 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA target strand; DNA non-target strand; Casx; Grna
- UniProt
- A0A357BT59
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 33% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA target strand | dna | 30 | — | — |
| D | DNA non-target strand | dna | 24 | — | — |
| Y | Casx | protein | 915 | 33% helix, 8% strand | A0A357BT59 |
| B | Grna | rna | 110 | — | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.74 | 0.86 | 39 | empty |
| 2 | 341 | 0.73 | 0.85 | 32 | empty |
| 3 | 52 | 0.69 | 0.98 | 14 | empty |
| 4 | 438 | 0.68 | 0.80 | 26 | empty |
| 5 | 56 | 0.67 | 0.96 | 15 | empty |
Interfaces
5 interfaces between chains.
- Y–B · 5214 Ų buried · 88 hydrogen bonds · protein-nucleic
- C–Y · 2315 Ų buried · 39 hydrogen bonds · protein-nucleic
- D–Y · 1901 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–B · 908 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- C–D · 451 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NY3 · CasX ternary complex with 30bp target DNA · 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 6NY3 · PDBe 6NY3 · UniProt A0A357BT59
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