Research workbench
2.9 ångströms resolution structure of the N-terminal domain of a variant surface glycoprotein from trypanosoma brucei
Analyse 2.9 ångströms resolution structure of the N-terminal domain of a variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VSG
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein mitat 1.2
- UniProt
- P26332
- Ligands
- NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Variant surface glycoprotein mitat 1.2 | protein | 362 | 52% helix, 10% strand | P26332 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.82 | 0.98 | 28 | empty |
| 2 | 216 | 0.51 | 0.76 | 34 | empty |
| 3 | 225 | 0.50 | 0.75 | 35 | empty |
| 4 | 147 | 0.43 | 0.75 | 34 | empty |
| 5 | 134 | 0.43 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4430 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1VSG · 2.9 ångströms resolution structure of the N-terminal domain of a variant surface… · 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 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 P26332
- Elsewhere: RCSB PDB 1VSG · PDBe 1VSG · UniProt P26332
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.