MolNFT v1 · #114124 · protein + DNA + RNA
Crystal structure of the streptococcus pyogenes CAS9 vrer variant in complex with sgrna and target DNA (tgcg pam)
5B2T · Guide RNA: “Crystal structure of the streptococcus pyogenes CAS9 vrer variant in complex with sgrna and target DNA (tgcg…”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.82). MolNFT v1 #114124 on GenesisL1…
- 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
- 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
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