MolNFT v1 · #102515 · protein + DNA + RNA
Crystal structure of streptococcus pyogenes CAS9 in complex with guide RNA and target DNA
4OO8 · CRISPR-associated endonuclease CAS9/CSN1: “Crystal structure of streptococcus pyogenes CAS9 in complex with guide RNA and target DNA”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #102515 on GenesisL1: 3D…
- 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
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