Research workbench
Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 preprocessed with protease alpha-Chymotrypsin
Analyse Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JDX
- Type
- protein
- Length
- 280 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Neisseria meningitidis 8013
- Molecule
- AcrIIC2; CRISPR-associated endonuclease Cas9
- EC
- 3.1.-.-
- UniProt
- A0A3E2QCQ3, C9X1G5
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · resolution 2.28 · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AcrIIC2 | protein | 121 | 28% helix, 29% strand | A0A3E2QCQ3 |
| B | AcrIIC2 | protein | 114 | 25% helix, 31% strand | A0A3E2QCQ3 |
| C | CRISPR-associated endonuclease Cas9 (EC 3.1.-.-) | protein | 45 | 49% helix, 2% strand | C9X1G5 |
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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.54 | 0.75 | 38 | empty |
| 2 | 126 | 0.44 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1397 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1333 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6JDX · Crystal structure of ACRIIC2 dimer in complex with partial NME1CAS9 preprocessed with… · the same entry in another collection · chain A against A, TM-score 1.00
- C9X1G5 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (C9X1G5) · a predicted model of the same protein · chain C against A, TM-score 0.51
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 A0A3E2QCQ3
- Every structure of UniProt C9X1G5
- Elsewhere: RCSB PDB 6JDX · PDBe 6JDX · UniProt A0A3E2QCQ3 · UniProt C9X1G5
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