Research workbench
Co-crystal structure of variant surface glycoprotein VSG2 in complex with nanobody VSG2(NB14)
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
- 7AQZ
- Type
- protein
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variant surface glycoprotein mitat 1.2; Nanobody VSG2(NB14)
- UniProt
- P26332
- Ligands
- NAG, BMA, MAN, NA
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.2 | protein | 358 | 52% helix, 9% strand | P26332 |
| B | Variant surface glycoprotein mitat 1.2 | protein | 361 | 52% helix, 9% strand | P26332 |
| C | Nanobody VSG2(NB14) | protein | 124 | 5% helix, 51% strand | — |
| D | Nanobody VSG2(NB14) | protein | 93 | 6% helix, 43% 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 · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B, C, A, D
- CIT · Citric acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.78 | 0.99 | 24 | CIT |
| 2 | 443 | 0.72 | 0.82 | 60 | CIT |
| 3 | 348 | 0.64 | 0.80 | 47 | CIT |
| 4 | 227 | 0.47 | 0.74 | 30 | empty |
| 5 | 186 | 0.44 | 0.74 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4546 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 776 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 645 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7AQZ · 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 7AQZ · PDBe 7AQZ · UniProt P26332
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