MolNFT v1 · #139025 · protein + DNA + RNA
Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target DNA (agaaaca pam)
5X2H · CRISPR-associated endonuclease CAS9: “Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target DNA (agaaaca pam)”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #139025 on GenesisL1: 3D…
- PDB
- 5X2H
- Type
- protein + DNA + RNA
- Length
- 875 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
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 | protein | 746 | 42% 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
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 | 611 | 0.79 | 0.85 | 71 | empty |
| 2 | 438 | 0.79 | 0.87 | 47 | EDO |
| 3 | 919 | 0.78 | 0.81 | 65 | empty |
| 4 | 846 | 0.78 | 0.82 | 52 | empty |
| 5 | 99 | 0.78 | 0.98 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5411 Ų buried · 112 hydrogen bonds · protein-nucleic
- A–C · 1876 Ų buried · 38 hydrogen bonds · protein-nucleic
- B–C · 988 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–D · 553 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 364 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 5X2H · 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 5X2H · PDBe 5X2H · UniProt Q0P897
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