Research workbench
Crystal structure of SPYCAS9-sgrna-ACRIIA4 ternary complex
Analyse Crystal structure of SPYCAS9-sgrna-ACRIIA4 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VW1
- Type
- protein + RNA
- Length
- 1,521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; Sgrna; Anti-CRISPR protein ACRIIA4
- EC
- 3.1.-.-
- UniProt
- Q99ZW2, A0A0E0UT28
- Ligands
- MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1362 | 48% helix, 12% strand | Q99ZW2 |
| C | Sgrna | rna | 73 | — | — |
| B | Anti-CRISPR protein ACRIIA4 | protein | 86 | 41% helix, 16% strand | A0A0E0UT28 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.87 | 0.88 | 129 | empty |
| 2 | 969 | 0.81 | 0.82 | 113 | EDO |
| 3 | 327 | 0.77 | 0.89 | 31 | PG4 |
| 4 | 982 | 0.77 | 0.80 | 72 | empty |
| 5 | 83 | 0.71 | 0.95 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–C · 5661 Ų buried · 143 hydrogen bonds · protein-nucleic
- A–B · 1837 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5VW1 · Crystal structure of SpyCas9-sgRNA-AcrIIA4 ternary complex · 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 A against A, TM-score 0.78
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
- Every structure of UniProt A0A0E0UT28
- Elsewhere: RCSB PDB 5VW1 · PDBe 5VW1 · UniProt Q99ZW2 · UniProt A0A0E0UT28
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.