Research workbench
Crystal structure of catalytically-active streptococcus pyogenes CRISPR-CAS9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage
Analyse Crystal structure of catalytically-active streptococcus pyogenes CRISPR-CAS9 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9R
- Type
- protein + DNA + RNA
- Length
- 1,527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; RNA (116-mer); DNA (30-mer); DNA (5'…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1362 | 44% helix, 10% strand | Q99ZW2 |
| A | RNA (116-mer) | rna | 116 | — | — |
| C | DNA (30-mer) | dna | 30 | — | — |
| D | DNA (5'- D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') | dna | 19 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.87 | 0.88 | 114 | empty |
| 2 | 956 | 0.83 | 0.85 | 86 | empty |
| 3 | 388 | 0.78 | 0.87 | 37 | empty |
| 4 | 960 | 0.76 | 0.79 | 100 | empty |
| 5 | 680 | 0.74 | 0.81 | 51 | SO4 |
Interfaces
5 interfaces between chains.
- B–A · 7008 Ų buried · 151 hydrogen bonds · protein-nucleic
- B–C · 1917 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–D · 1528 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–C · 1025 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- C–D · 481 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5F9R · Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex… · the same entry in another collection · chain B against B, 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 0.88
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 5F9R · PDBe 5F9R · UniProt Q99ZW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.