Research workbench
Crystal structure of VSG13 soaked in 0.5 M used to phase VSG13 to solve the structure.
Analyse Crystal structure of VSG13 soaked in 0.5 M used to phase VSG13 to solve the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z8G
- Type
- protein
- Length
- 695 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, BR, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.13 | protein | 346 | 52% helix, 12% strand | Q58NS4 |
| B | Variant surface glycoprotein mitat 1.13 | protein | 349 | 51% 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 B, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, A
- BR · Bromide ion · ion · 23 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.96 | 22 | BR |
| 2 | 358 | 0.68 | 0.81 | 36 | BR |
| 3 | 191 | 0.57 | 0.80 | 27 | SO4, BR |
| 4 | 63 | 0.39 | 0.79 | 26 | empty |
| 5 | 70 | 0.30 | 0.74 | 17 | NAG |
Interfaces
1 interface between chains.
- A–B · 4136 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z8G · Crystal structure of VSG13 soaked in 0.5 M used to phase VSG13 to solve the structure. · 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 6Z8G · PDBe 6Z8G · UniProt Q58NS4
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