Research workbench
Crystal structure of the type II-C CAS9 enzyme from actinomyces naeslundii
Analyse Crystal structure of the type II-C CAS9 enzyme from actinomyces naeslundii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OGC
- Type
- protein
- Length
- 883 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnh endonuclease domain protein
- UniProt
- J3F2B0
- Ligands
- SPD, MN, MG, ZN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnh endonuclease domain protein | protein | 883 | 39% helix, 17% strand | J3F2B0 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.81 | 0.82 | 105 | empty |
| 2 | 673 | 0.67 | 0.76 | 52 | MN |
| 3 | 106 | 0.51 | 0.82 | 21 | empty |
| 4 | 135 | 0.48 | 0.79 | 27 | empty |
| 5 | 102 | 0.47 | 0.80 | 22 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4OGC · Crystal structure of the Type II-C Cas9 enzyme from Actinomyces naeslundii · the same entry in another collection · chain A against A, TM-score 1.00
- J3F2B0 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (J3F2B0) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 J3F2B0
- Elsewhere: RCSB PDB 4OGC · PDBe 4OGC · UniProt J3F2B0
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