Research workbench
Variant surface glycoprotein vsgsur bound to suramin
Analyse Variant surface glycoprotein vsgsur bound to suramin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z7B
- Type
- protein
- Length
- 758 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein sur
- UniProt
- A0A291L8F4
- Ligands
- SVR, MAN, NAG, BMA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein sur | protein | 380 | 50% helix, 16% strand | A0A291L8F4 |
| B | Variant surface glycoprotein sur | protein | 378 | 50% helix, 18% strand | A0A291L8F4 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.79 | 0.83 | 70 | empty |
| 2 | 197 | 0.54 | 0.78 | 20 | NAG |
| 3 | 169 | 0.52 | 0.79 | 20 | NAG |
| 4 | 51 | 0.24 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3795 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z7B · Variant Surface Glycoprotein VSGsur bound to suramin · 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 A0A291L8F4
- Elsewhere: RCSB PDB 6Z7B · PDBe 6Z7B · UniProt A0A291L8F4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.