MolNFT v1 · #27228 · protein

Structure of plasmepsin II in complex with pepstatin a

1XDH · Plasmepsin 2: “Structure of plasmepsin II in complex with pepstatin a”. X-ray diffraction, 1 ligand (IVA), 5 pockets (best druggability 0.77). MolNFT v1 #27228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XDH
Type: protein
Length: 668 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasmepsin 2; Pepstatin
EC: 3.4.23.39
UniProt: P46925
Ligands: IVA
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plasmepsin 2 (EC 3.4.23.39)	protein	329	14% helix, 48% strand	P46925
C, D	Pepstatin	protein	5	0% helix, 40% strand	—

Ligands and binding sites

IVA · Isovaleric acid · ligand · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.77	0.79	79	IVA
2	177	0.51	0.78	27	empty
3	156	0.50	0.78	38	empty
4	97	0.42	0.78	24	empty
5	50	0.25	0.73	11	empty

Interfaces

5 interfaces between chains.

A–B · 1289 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 606 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 596 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 52 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, covalent ligand).

Compared structures

1XDH · Structure of plasmepsin II in complex with pepstatin A · 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 0.90

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 P46925
Elsewhere: RCSB PDB 1XDH · PDBe 1XDH · UniProt P46925

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