MolNFT v1 · #184863 · protein
Variant surface glycoprotein 2 (VSG2, MITAT1.2, VSG221) bound to calcium
7P56 · Variant surface glycoprotein mitat 1.2: “Variant surface glycoprotein 2 (VSG2, MITAT1.2, VSG221) bound to calcium”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 7 pockets (best druggability 0.82). MolNFT v1 #184863 on GenesisL1: 3D…
- PDB
- 7P56
- Type
- protein
- Length
- 680 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, CA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.2 | protein | 346 | 51% helix, 10% strand | P26332 |
| B | Variant surface glycoprotein mitat 1.2 | protein | 334 | 51% 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 · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.82 | 0.98 | 26 | empty |
| 2 | 201 | 0.49 | 0.75 | 33 | empty |
| 3 | 90 | 0.41 | 0.78 | 31 | empty |
| 4 | 109 | 0.40 | 0.76 | 24 | empty |
| 5 | 93 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3874 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7P56 · Variant Surface Glycoprotein 2 (VSG2, MiTat1.2, VSG221) Bound to Calcium · 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 B 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 7P56 · PDBe 7P56 · UniProt P26332
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