MolNFT v1 · #110676 · protein

Endothiapepsin in complex with fragment 207

4Y3T: “Endothiapepsin in complex with fragment 207”. X-ray diffraction, 2 ligands (46H, 46J), 2 pockets (best druggability 0.58). MolNFT v1 #110676 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Y3T
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: 46H, 46J
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endothiapepsin (EC 3.4.23.22)	protein	330	11% helix, 45% strand	P11838

Ligands and binding sites

46H · (3S)-piperidin-3-yl(piperidin-1-yl)methanone · ligand · 2 copies · chains A
46J · (3R)-piperidin-3-yl(piperidin-1-yl)methanone · ligand · chains A
GOL · Glycerol · additive · 6 copies · chains A
DMS · Dimethyl sulfoxide · additive · 6 copies · chains A
ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

2 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	321	0.58	0.76	38	DMS, 46J, 46H
2	50	0.30	0.77	14	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4Y3T · Endothiapepsin in complex with fragment 207 · 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 4Y3T · PDBe 4Y3T · UniProt P11838

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