MolNFT v1 · #117200 · protein
Crystal structure of eosinophil-derived neurotoxin in complex with the triazole double-headed ribonucleoside 11C
5E13 · Non-secretory ribonuclease: “Crystal structure of eosinophil-derived neurotoxin in complex with the triazole double-headed ribonucleoside…”. X-ray diffraction, 1 ligand (5J9), 1 pocket (best druggability 0.29). MolNFT v1 #117200 on…
- PDB
- 5E13
- Type
- protein
- Length
- 135 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-secretory ribonuclease
- EC
- 3.1.27.5
- UniProt
- P10153
- Ligands
- 5J9
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-secretory ribonuclease (EC 3.1.27.5) | protein | 135 | 24% helix, 35% strand | P10153 |
Ligands and binding sites
- 5J9 · 3'-{4-[(4-amino-2-oxopyrimidin-1(2H)-yl)methyl]-1H-1,2,3-triazol-1-yl}-3'-deoxyadenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.29 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5E13 · Crystal structure of Eosinophil-derived neurotoxin in complex with the triazole… · the same entry in another collection · chain A against A, TM-score 1.00
- P10153 · AlphaFold monomer V2.0 prediction for non-secretory ribonuclease (P10153) · 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 P10153
- Elsewhere: RCSB PDB 5E13 · PDBe 5E13 · UniProt P10153
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