Research workbench
Crystal structure of NME2CAS9 in complex with sgrna and target DNA (aggccc pam)
Analyse Crystal structure of NME2CAS9 in complex with sgrna and target DNA (aggccc pam) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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