MolNFT v1 · #88492 · protein
High-glycosylation crystal structure of the bifunctional endonuclease (ATBFN2) from arabidopsis thaliana
4CWM · Endonuclease 2: “High-glycosylation crystal structure of the bifunctional endonuclease (ATBFN2) from arabidopsis thaliana”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.76). MolNFT v1 #88492 on…
- PDB
- 4CWM
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease 2
- EC
- 3.1.30.1
- UniProt
- Q9C9G4
- Ligands
- NAG, BMA, MAN, ZN
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease 2 (EC 3.1.30.1) | protein | 256 | 64% helix, 7% strand | Q9C9G4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.76 | 0.80 | 68 | empty |
| 2 | 87 | 0.46 | 0.81 | 13 | empty |
| 3 | 89 | 0.37 | 0.77 | 23 | empty |
| 4 | 75 | 0.34 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4CWM · High-glycosylation crystal structure of the bifunctional endonuclease (AtBFN2) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C9G4 · AlphaFold monomer V2.0 prediction for endonuclease 2 (Q9C9G4) · a predicted model of the same protein · 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
- Every structure of UniProt Q9C9G4
- Elsewhere: RCSB PDB 4CWM · PDBe 4CWM · UniProt Q9C9G4
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