Research workbench
Co-crystal structure of variant surface glycoprotein VSG2 in complex with nanobody VSG2(NB19)
Analyse Co-crystal structure of variant surface glycoprotein VSG2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AR0
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein mitat 1.2; Nanobody VSG2(NB19)
- UniProt
- P26332
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.2 | protein | 359 | 51% helix, 9% strand | P26332 |
| B | Nanobody VSG2(NB19) | protein | 125 | 15% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.48 | 0.80 | 21 | empty |
| 2 | 101 | 0.37 | 0.75 | 24 | empty |
| 3 | 52 | 0.30 | 0.76 | 15 | NAG |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7AR0 · Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody… · the same entry in another collection · chain A against A, TM-score 1.00
- P26332 · AlphaFold monomer V2.0 prediction for variant surface glycoprotein mitat 1.2 (P26332) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P26332
- Elsewhere: RCSB PDB 7AR0 · PDBe 7AR0 · UniProt P26332
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