Research workbench
CAS9:SGRNA:DNA (S. pyogenes) forming a 3-base-pair R-loop
Analyse CAS9:SGRNA:DNA (S. pyogenes) forming a 3-base-pair R-loop in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S38
- Type
- protein + DNA + RNA
- Length
- 1,492 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-target DNA strand; CRISPR-associated endonuclease CAS9/CSN1; Single-guide RNA; Target…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Non-target DNA strand | dna | 26 | — | — |
| P | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1353 | 47% helix, 12% strand | Q99ZW2 |
| R | Single-guide RNA | rna | 87 | — | — |
| T | Target DNA strand | dna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.80 | 0.81 | 103 | empty |
| 2 | 1013 | 0.78 | 0.81 | 89 | empty |
| 3 | 575 | 0.75 | 0.82 | 58 | empty |
| 4 | 76 | 0.74 | 0.98 | 23 | empty |
| 5 | 86 | 0.72 | 0.96 | 22 | empty |
Interfaces
5 interfaces between chains.
- P–R · 6453 Ų buried · 143 hydrogen bonds · protein-nucleic
- N–T · 1101 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- N–P · 840 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 729 Ų buried · 16 hydrogen bonds · protein-nucleic
- R–T · 201 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7S38 · Cas9:sgRNA:DNA (S. pyogenes) forming a 3-base-pair R-loop · the same entry in another collection · chain N against N, 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 P against A, TM-score 0.84
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 7S38 · PDBe 7S38 · UniProt Q99ZW2
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