GL1X · GenesisL1 explorer

MolNFT v1 · #27251 · protein

Structure of plasmepsin II in complex of an pepstatin analogue

1XE6 · Plasmepsin 2: “Structure of plasmepsin II in complex of an pepstatin analogue”. X-ray diffraction, 1 ligand (5FP), 3 pockets (best druggability 0.83). MolNFT v1 #27251 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1XE6
Type
protein
Length
658 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Plasmepsin 2
EC
3.4.23.39
UniProt
P46925
Ligands
5FP
Pockets
3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 44% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BPlasmepsin 2 (EC 3.4.23.39)protein32913% helix, 44% strandP46925

Ligands and binding sites

  • 5FP · 5,5,5-trifluoro-3-hydroxy-4-[2-(5,5,5-trifluoro-3-hydroxy-4-{3-methyl-2-[3-methyl-2-(3-methyl-butyrylamino)-butyrylamino]-butyrylamino}-pentanoylamino)-propionylamino]-pentanoic acid · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19630.830.83975FP
22490.590.7931empty
31310.460.7828empty

Interfaces

1 interface between chains.

  • A–B · 1322 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

  • 1XE6 · Structure of plasmepsin II in complex of an pepstatin analogue · the same entry in another collection · chain A against A, TM-score 1.00
  • P46925 · AlphaFold monomer V2.0 prediction for plasmepsin-2 (P46925) · a predicted model of the same protein · chain A against A, TM-score 0.91

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