MolNFT v1 · #184864 · protein
VSG2 mutant structure lacking the calcium binding pocket
7P57 · Variant surface glycoprotein mitat 1.2: “VSG2 mutant structure lacking the calcium binding pocket”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 1 pocket (best druggability 0.49). MolNFT v1 #184864 on GenesisL1: 3D structure…
- PDB
- 7P57
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- 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
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Variant surface glycoprotein mitat 1.2 | protein | 359 | 52% helix, 9% strand | P26332 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.49 | 0.78 | 33 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7P57 · VSG2 mutant structure lacking the calcium binding pocket · 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 7P57 · PDBe 7P57 · UniProt P26332
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