MolNFT v1 · #139391 · protein
Structure of the envelope glycoprotein of dhori virus
5XEB: “Structure of the envelope glycoprotein of dhori virus”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.47). MolNFT v1 #139391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XEB
- Type
- protein
- Length
- 1,169 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- P27427
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Envelope glycoprotein | protein | 390 | 23% helix, 33% strand | P27427 |
| C | Envelope glycoprotein | protein | 389 | 23% helix, 33% strand | P27427 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.47 | 0.73 | 31 | empty |
| 2 | 181 | 0.46 | 0.75 | 35 | empty |
| 3 | 142 | 0.40 | 0.73 | 22 | empty |
| 4 | 99 | 0.39 | 0.76 | 20 | empty |
| 5 | 101 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 554 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XEB · Structure of the envelope glycoprotein of Dhori virus · the same entry in another collection · 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 P27427
- Elsewhere: RCSB PDB 5XEB · PDBe 5XEB · UniProt P27427
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