Research workbench
Conformational states of CAS9-sgrna-DNA ternary complex in the presence of magnesium
Analyse Conformational states of CAS9-sgrna-DNA ternary complex in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O0X
- Type
- protein + DNA + RNA
- Length
- 1,262 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; Single guide RNA; 5' product of target strand…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1112 | 45% helix, 11% strand | Q99ZW2 |
| B | Single guide RNA | rna | 98 | — | — |
| C | 5' product of target strand DNA | dna | 13 | — | — |
| D | Non-target strand DNA | dna | 16 | — | — |
| c | 3' product of target strand DNA | dna | 23 | — | — |
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 | 689 | 0.78 | 0.83 | 57 | empty |
| 2 | 933 | 0.77 | 0.80 | 99 | empty |
| 3 | 465 | 0.75 | 0.84 | 71 | empty |
| 4 | 820 | 0.74 | 0.79 | 94 | empty |
| 5 | 199 | 0.71 | 0.88 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 6091 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–c · 984 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–c · 883 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–D · 538 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 488 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 6O0X · Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q99ZW2
- Elsewhere: RCSB PDB 6O0X · PDBe 6O0X · UniProt Q99ZW2
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