Research workbench
Crystal structure of SPYCAS9 variant vqr bound to sgrna and tgag pam target DNA
Analyse Crystal structure of SPYCAS9 variant vqr bound to sgrna and tgag pam target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FW1
- Type
- protein + DNA + RNA
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1304 | 50% helix, 12% strand | Q99ZW2 |
| C | Target DNA strand | dna | 28 | — | — |
| D | Non-target DNA strand | dna | 11 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 13 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.83 | 0.85 | 111 | K, MG |
| 2 | 672 | 0.77 | 0.83 | 52 | empty |
| 3 | 766 | 0.72 | 0.79 | 53 | empty |
| 4 | 318 | 0.66 | 0.82 | 33 | empty |
| 5 | 303 | 0.65 | 0.81 | 47 | K |
Interfaces
5 interfaces between chains.
- A–B · 6055 Ų buried · 141 hydrogen bonds · protein-nucleic
- B–C · 1734 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 970 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- B–D · 631 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 386 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 5FW1 · Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA · 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 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 5FW1 · PDBe 5FW1 · UniProt Q99ZW2
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