MolNFT v1 · #139390 · protein
Structure of thogoto virus envelope glycoprotein
5XEA: “Structure of thogoto virus envelope glycoprotein”. X-ray diffraction, 2 ligands (NAG, BMA), 14 pockets (best druggability 0.85). MolNFT v1 #139390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XEA
- Type
- protein
- Length
- 1,169 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- P28977
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein | protein | 385 | 24% helix, 38% strand | P28977 |
| B | Envelope glycoprotein | protein | 397 | 24% helix, 36% strand | P28977 |
| C | Envelope glycoprotein | protein | 387 | 25% helix, 38% strand | P28977 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.85 | 0.86 | 84 | empty |
| 2 | 1001 | 0.74 | 0.77 | 91 | empty |
| 3 | 352 | 0.57 | 0.75 | 40 | empty |
| 4 | 337 | 0.56 | 0.75 | 32 | empty |
| 5 | 320 | 0.55 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5674 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 5566 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 5487 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5XEA · Structure of Thogoto virus envelope glycoprotein · 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 P28977
- Elsewhere: RCSB PDB 5XEA · PDBe 5XEA · UniProt P28977
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