Research workbench
Crystal structure of the streptococcus pyogenes CAS9 vqr variant in complex with sgrna and target DNA (tga pam)
Analyse Crystal structure of the streptococcus pyogenes CAS9 vqr variant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B2R
- Type
- protein + DNA + RNA
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guide RNA; CRISPR-associated endonuclease CAS9; Target DNA; Non-target DNA, DNA…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guide RNA | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1319 | 49% helix, 12% strand | Q99ZW2 |
| C | Target DNA | dna | 28 | — | — |
| D | Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 11 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.81 | 0.83 | 106 | K, MG |
| 2 | 581 | 0.73 | 0.81 | 78 | K |
| 3 | 92 | 0.69 | 0.93 | 24 | empty |
| 4 | 558 | 0.69 | 0.79 | 29 | empty |
| 5 | 657 | 0.67 | 0.76 | 81 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5872 Ų buried · 131 hydrogen bonds · protein-nucleic
- B–C · 1536 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 1015 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- B–D · 577 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 362 Ų buried · 26 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 5B2R · PDBe 5B2R · UniProt Q99ZW2
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