Research workbench
Crystal structure of CAS9 bound to pam-containing DNA target containing mismatches at positions 1-3
Analyse Crystal structure of CAS9 bound to pam-containing DNA target containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UN5
- Type
- protein + DNA + RNA
- Length
- 1,426 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand proximal fragment…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1310 | 48% helix, 11% strand | Q99ZW2 |
| C | Target DNA strand proximal fragment | dna | 8 | — | — |
| D | Non-target DNA strand | dna | 10 | — | — |
| E | Target DNA strand distal fragment | dna | 17 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.81 | 0.82 | 93 | MG |
| 2 | 688 | 0.77 | 0.83 | 59 | empty |
| 3 | 108 | 0.70 | 0.93 | 24 | empty |
| 4 | 854 | 0.69 | 0.76 | 78 | empty |
| 5 | 575 | 0.69 | 0.78 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5917 Ų buried · 113 hydrogen bonds · protein-nucleic
- B–E · 1190 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–E · 829 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- B–D · 563 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 378 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 4UN5 · Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at… · 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 0.98
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 4UN5 · PDBe 4UN5 · UniProt Q99ZW2
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