MolNFT v1 · #107789 · protein + DNA + RNA
Crystal structure of CAS9 bound to pam-containing DNA target
4UN3 · Sgrna: “Crystal structure of CAS9 bound to pam-containing DNA target”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #107789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UN3
- Type
- protein + DNA + RNA
- Length
- 1,426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1306 | 49% helix, 12% strand | Q99ZW2 |
| C | Target DNA strand | dna | 28 | — | — |
| D | Non-target DNA strand | dna | 11 | — | — |
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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.83 | 0.85 | 107 | MG |
| 2 | 718 | 0.77 | 0.83 | 62 | MG |
| 3 | 883 | 0.73 | 0.78 | 70 | empty |
| 4 | 389 | 0.64 | 0.79 | 33 | empty |
| 5 | 123 | 0.63 | 0.87 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6055 Ų buried · 131 hydrogen bonds · protein-nucleic
- B–C · 1737 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 977 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- B–D · 590 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 387 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 4UN3 · Crystal structure of Cas9 bound to PAM-containing DNA target · 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 4UN3 · PDBe 4UN3 · UniProt Q99ZW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.