MolNFT v1 · #102256 · protein
Crystal structure of the type II-C CAS9 enzyme from actinomyces naeslundii
4OGE · Hnh endonuclease domain protein: “Crystal structure of the type II-C CAS9 enzyme from actinomyces naeslundii”. X-ray diffraction, 3 ligands (SPD, MG, ZN), 11 pockets (best druggability 0.82). MolNFT v1 #102256 on GenesisL1: 3D…
- PDB
- 4OGE
- Type
- protein
- Length
- 977 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnh endonuclease domain protein
- UniProt
- J3F2B0
- Ligands
- SPD, MG, ZN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnh endonuclease domain protein | protein | 977 | 40% helix, 16% strand | J3F2B0 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.82 | 0.83 | 96 | empty |
| 2 | 438 | 0.64 | 0.78 | 41 | SPD |
| 3 | 519 | 0.62 | 0.75 | 55 | empty |
| 4 | 447 | 0.61 | 0.76 | 47 | MG |
| 5 | 431 | 0.61 | 0.76 | 50 | empty |
Compared structures
- 4OGE · 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 0.79
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 4OGE · PDBe 4OGE · UniProt J3F2B0
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