Research workbench

Porcine pepsin in complex with ritonavir

Analyse Porcine pepsin in complex with ritonavir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XCY
Type: protein
Length: 325 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pepsin a
EC: 3.4.23.1
UniProt: P00791
Ligands: RIT
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pepsin a (EC 3.4.23.1)	protein	325	15% helix, 45% strand	P00791

Ligands and binding sites

RIT · Ritonavir · ligand · 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	380	0.67	0.80	54	RIT
2	72	0.33	0.76	17	empty

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, phosphorylation).

Compared structures

6XCY · Porcine pepsin in complex with ritonavir · the same entry in another collection · chain A against A, TM-score 1.00
P00791 · AlphaFold monomer V2.0 prediction for pepsin a (P00791) · a predicted model of the same protein · chain A 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 P00791
Elsewhere: RCSB PDB 6XCY · PDBe 6XCY · UniProt P00791

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