MolNFT v1 · #139024 · protein + DNA + RNA
Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target DNA (agaaacc pam)
5X2G · CRISPR-associated endonuclease CAS9: “Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target DNA (agaaacc pam)”. X-ray diffraction, 18 pockets (best druggability 0.81). MolNFT v1 #139024 on GenesisL1: 3D…
- PDB
- 5X2G
- Type
- protein + DNA + RNA
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Sgrna; Target DNA strand; Non-target DNA strand
- UniProt
- Q0P897
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 | protein | 749 | 41% helix, 17% strand | Q0P897 |
| B | Sgrna | rna | 93 | — | — |
| C | Target DNA strand | dna | 28 | — | — |
| D | Non-target DNA strand | dna | 8 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.81 | 0.83 | 83 | empty |
| 2 | 864 | 0.79 | 0.82 | 56 | empty |
| 3 | 98 | 0.78 | 0.98 | 21 | empty |
| 4 | 474 | 0.77 | 0.86 | 49 | EDO |
| 5 | 1117 | 0.76 | 0.79 | 76 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5425 Ų buried · 110 hydrogen bonds · protein-nucleic
- A–C · 1763 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 985 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–D · 614 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 358 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 5X2G · Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0P897 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (Q0P897) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q0P897
- Elsewhere: RCSB PDB 5X2G · PDBe 5X2G · UniProt Q0P897
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