Research workbench
Crystal structure of variant surface glycoprotein VSG13
Analyse Crystal structure of variant surface glycoprotein VSG13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z8H
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein mitat 1.13
- UniProt
- Q58NS4
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.13 | protein | 351 | 52% helix, 12% strand | Q58NS4 |
| B | Variant surface glycoprotein mitat 1.13 | protein | 350 | 52% helix, 13% strand | Q58NS4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 567 | 0.73 | 0.81 | 61 | SO4 |
| 2 | 118 | 0.43 | 0.77 | 15 | empty |
| 3 | 58 | 0.30 | 0.76 | 20 | empty |
| 4 | 67 | 0.30 | 0.75 | 18 | NAG |
Interfaces
1 interface between chains.
- A–B · 4142 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z8H · Crystal structure of Variant Surface Glycoprotein VSG13 · 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 Q58NS4
- Elsewhere: RCSB PDB 6Z8H · PDBe 6Z8H · UniProt Q58NS4
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