Research workbench
Crystal structure of streptococcus pyogenes CAS9 in complex with guide RNA and target DNA
Analyse Crystal structure of streptococcus pyogenes CAS9 in complex with guide RNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OO8
- Type
- protein + DNA + RNA
- Length
- 2,700 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; RNA (97-mer); DNA (5'…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1301 | 48% helix, 12% strand | Q99ZW2 |
| B, E | RNA (97-mer) | rna | 97 | — | — |
| C | DNA (5'- D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP* C)-3') | dna | 20 | — | — |
| D | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1163 | 46% helix, 13% strand | Q99ZW2 |
| F | DNA (5'- D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP* C)-3') | dna | 22 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.82 | 0.84 | 81 | empty |
| 2 | 880 | 0.81 | 0.83 | 83 | empty |
| 3 | 1111 | 0.80 | 0.82 | 90 | empty |
| 4 | 1156 | 0.78 | 0.80 | 104 | empty |
| 5 | 714 | 0.77 | 0.82 | 90 | empty |
Interfaces
8 interfaces between chains.
- A–B · 6904 Ų buried · 150 hydrogen bonds · protein-nucleic
- D–E · 6585 Ų buried · 145 hydrogen bonds · protein-nucleic
- A–C · 1416 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–F · 1136 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 1008 Ų buried · 95 hydrogen bonds · nucleic-nucleic
Compared structures
- 4OO8 · Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA · the same entry in another collection · chain F against F, 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 0.95
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 4OO8 · PDBe 4OO8 · UniProt Q99ZW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.