MolNFT v1 · #184868 · protein
Variant surface glycoprotein 3 (VSG3, MITAT1.3, VSG224) mutant (serine 319 to alanine), single O-linked glycosylated at SER317
7P5B: “Variant surface glycoprotein 3 (VSG3, MITAT1.3, VSG224) mutant (serine 319 to alanine), single O-linked…”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 2 pockets (best druggability 0.37). MolNFT v1 #184868 on GenesisL1: 3D…
- PDB
- 7P5B
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein
- UniProt
- B3GVK1
- Ligands
- MAN, NAG, BMA, GLC
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein | protein | 358 | 53% helix, 4% strand | B3GVK1 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.37 | 0.75 | 14 | NAG |
| 2 | 50 | 0.23 | 0.72 | 12 | empty |
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7P5B · Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 319 to alanine)… · 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 B3GVK1
- Elsewhere: RCSB PDB 7P5B · PDBe 7P5B · UniProt B3GVK1
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