MolNFT v1 · #153484 · protein + DNA + RNA
Crystal structure of NME2CAS9 in complex with sgrna and target DNA (aggccc pam)
6JFU · CRISPR-associated endonuclease CAS9: “Crystal structure of NME2CAS9 in complex with sgrna and target DNA (aggccc pam)”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #153484 on GenesisL1: 3D structure, binding…
- PDB
- 6JFU
- Type
- protein + DNA + RNA
- Length
- 1,035 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Sgrna; Target-strand DNA; Non-target strand
- EC
- 3.1.-.-
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 884 | 37% helix, 14% strand | — |
| B | Sgrna | rna | 105 | — | — |
| C | Target-strand DNA | dna | 35 | — | — |
| D | Non-target strand | dna | 11 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.86 | 0.91 | 55 | empty |
| 2 | 631 | 0.85 | 0.90 | 84 | empty |
| 3 | 710 | 0.82 | 0.86 | 88 | empty |
| 4 | 878 | 0.78 | 0.81 | 123 | empty |
| 5 | 230 | 0.77 | 0.91 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5381 Ų buried · 118 hydrogen bonds · protein-nucleic
- A–C · 1990 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 1137 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–D · 612 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 485 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6JFU · Crystal structure of Nme2Cas9 in complex with sgRNA and target DNA (AGGCCC PAM) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6JFU · PDBe 6JFU
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