MolNFT v1 · #29004 · protein

The plasmodium falciparum cysteine protease falcipain-2

1YVB · Falcipain 2: “The plasmodium falciparum cysteine protease falcipain-2”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #29004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YVB
Type: protein
Length: 352 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Falcipain 2; Cystatin
EC: 3.4.22.-
UniProt: Q9N6S8, P01038
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Falcipain 2 (EC 3.4.22.-)	protein	241	26% helix, 24% strand	Q9N6S8
I	Cystatin	protein	111	18% helix, 40% strand	P01038

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.52	0.81	27	empty
2	167	0.48	0.77	31	empty
3	76	0.34	0.76	13	empty

Interfaces

1 interface between chains.

A–I · 922 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

1YVB · the Plasmodium falciparum Cysteine Protease Falcipain-2 · the same entry in another collection · chain A against A, TM-score 1.00
P01038 · AlphaFold monomer V2.0 prediction for cystatin (P01038) · a predicted model of the same protein · chain I against A, TM-score 0.96

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 Q9N6S8
Every structure of UniProt P01038
Elsewhere: RCSB PDB 1YVB · PDBe 1YVB · UniProt Q9N6S8 · UniProt P01038

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