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One chain form of the 66.3 kda protein

Analyse One chain form of the 66.3 kda protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3FGW
Type
protein
Length
529 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Putative phospholipase B-like 2
EC
3.1.1.-
UniProt
Q3TCN2
Ligands
NAG, BMA, NA, IOD
Pockets
5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APutative phospholipase B-like 2 (EC 3.1.1.-)protein52931% helix, 22% strandQ3TCN2

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
  • BMA · beta-D-mannopyranose · sugar
  • NA · Sodium ion · metal · chains A
  • IOD · Iodide ion · ion · 7 copies · chains A
  • GOL · Glycerol · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16230.730.8060empty
2710.400.7912empty
3970.380.7519empty
4700.360.7717IOD
5510.300.7612empty

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

  • 3FGW · One chain form of the 66.3 kDa protein · the same entry in another collection · chain A against A, TM-score 1.00
  • Q3TCN2 · AlphaFold monomer V2.0 prediction for putative phospholipase B-like 2 (Q3TCN2) · a predicted model of the same protein · chain A against A, TM-score 1.00

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