MolNFT v1 · #75613 · protein

Secreted aspartic protease 2 in complex with benzamidine

3PVK · Candidapepsin-2: “Secreted aspartic protease 2 in complex with benzamidine”. X-ray diffraction, 2 ligands (BEN, ZN), 1 pocket (best druggability 0.50). MolNFT v1 #75613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PVK
Type: protein
Length: 330 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Candidapepsin-2
EC: 3.4.23.24
UniProt: P28871
Ligands: BEN, ZN
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Candidapepsin-2 (EC 3.4.23.24)	protein	330	10% helix, 49% strand	P28871

Ligands and binding sites

BEN · Benzamidine · ligand · 2 copies · chains A
ZN · Zinc ion · metal · chains A
IMD · Imidazole · additive · 2 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.50	0.74	34	BEN, MPD

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3PVK · Secreted aspartic protease 2 in complex with benzamidine · the same entry in another collection · 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 P28871
Elsewhere: RCSB PDB 3PVK · PDBe 3PVK · UniProt P28871

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