Research workbench
Crystal structure of the streptococcus pyogenes CAS9 vrer variant in complex with sgrna and target DNA (tgcg pam)
Analyse Crystal structure of the streptococcus pyogenes CAS9 vrer 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
- 5B2T
- Type
- protein + DNA + RNA
- Length
- 1,443 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 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% 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 | 1326 | 48% helix, 12% strand | Q99ZW2 |
| C | Target DNA | dna | 28 | — | — |
| D | Non-target DNA, DNA (5'-D(*TP*GP*CP*GP*AP*TP*TP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 10 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.82 | 0.83 | 105 | K, MG |
| 2 | 1006 | 0.78 | 0.80 | 85 | K, ACT |
| 3 | 573 | 0.70 | 0.80 | 30 | empty |
| 4 | 114 | 0.68 | 0.91 | 24 | empty |
| 5 | 444 | 0.64 | 0.78 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5978 Ų buried · 129 hydrogen bonds · protein-nucleic
- B–C · 1513 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1010 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- B–D · 612 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 367 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Compared structures
- 5B2T · Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA… · 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 0.99
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 5B2T · PDBe 5B2T · UniProt Q99ZW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.