Research workbench
Co-crystal structure of variant surface glycoprotein VSG2 in complex with nanobody VSG2(NB9)
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
- 7AQX
- Type
- protein
- Length
- 939 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein mitat 1.2; Nanobody VSG2(NB9)
- UniProt
- P26332
- Ligands
- NAG, BMA, MAN, NA
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Variant surface glycoprotein mitat 1.2 | protein | 362 | 51% helix, 9% strand | P26332 |
| C | Nanobody VSG2(NB9) | protein | 116 | 5% helix, 51% strand | — |
| D | Nanobody VSG2(NB9) | protein | 99 | 6% helix, 52% strand | — |
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 · chains B
- NA · Sodium ion · metal · 2 copies · chains A, C, B, D
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 24 | CIT |
| 2 | 477 | 0.68 | 0.79 | 58 | empty |
| 3 | 360 | 0.68 | 0.82 | 46 | empty |
| 4 | 474 | 0.67 | 0.79 | 66 | empty |
| 5 | 316 | 0.52 | 0.74 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4432 Ų buried · 63 hydrogen bonds · protein-protein
- B–D · 720 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 709 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7AQX · 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 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 7AQX · PDBe 7AQX · UniProt P26332
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