MolNFT v1 · #131664 · protein

Crystal structure of endothiapepsin-FRG081 complex

5QB9: “Crystal structure of endothiapepsin-FRG081 complex”. X-ray diffraction, 1 ligand (D6S), 1 pocket (best druggability 0.57). MolNFT v1 #131664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QB9
Type: protein
Length: 330 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endothiapepsin
EC: 3.4.23.22
UniProt: P11838
Ligands: D6S
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endothiapepsin (EC 3.4.23.22)	protein	330	10% helix, 45% strand	P11838

Ligands and binding sites

D6S · (1S,2S,3S,4R,5R)-2-amino-4-[benzyl(methyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol · ligand · chains A
GOL · Glycerol · additive · 3 copies · chains A
ACT · Acetate ion · 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	323	0.57	0.76	33	D6S

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5QB9 · Crystal structure of Endothiapepsin-FRG081 complex · the same entry in another collection · chain A against A, TM-score 1.00
P11838 · AlphaFold monomer V2.0 prediction for endothiapepsin (P11838) · a predicted model of the same protein · 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 P11838
Elsewhere: RCSB PDB 5QB9 · PDBe 5QB9 · UniProt P11838

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