Research workbench
SpCas9 bound to TRAC off-target2 DNA substrate
Analyse SpCas9 bound to TRAC off-target2 DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QR1
- Type
- protein + DNA + RNA
- Length
- 1,447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Streptococcus pyogenes; SYNTHETIC CONSTRUCT
- Molecule
- TRAC sgRNA; CRISPR-associated endonuclease Cas9/Csn1; TRAC off-target2 target strand…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.6 · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRAC sgRNA | rna | 81 | — | — |
| B | CRISPR-associated endonuclease Cas9/Csn1 (EC 3.1.-.-) | protein | 1328 | 49% helix, 12% strand | Q99ZW2 |
| C | TRAC off-target2 target strand | dna | 28 | — | — |
| D | TRAC off-target2 non-target strand | dna | 10 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 14 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1090 | 0.77 | 0.79 | 111 | K |
| 2 | 637 | 0.74 | 0.81 | 61 | empty |
| 3 | 505 | 0.73 | 0.82 | 40 | MG, K |
| 4 | 319 | 0.72 | 0.85 | 44 | K |
| 5 | 445 | 0.70 | 0.82 | 49 | K |
Interfaces
5 interfaces between chains.
- A–B · 6090 Ų buried · 137 hydrogen bonds · protein-nucleic
- B–C · 1758 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1013 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–D · 571 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 391 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 7QR1 · PDBe 7QR1 · UniProt Q99ZW2
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