Research workbench

Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in complex with the N-terminal octapeptide of the propeptid

Analyse Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N70
Type: protein
Length: 347 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cathepsin D; Ala-phe-arg-ile-pro-leu-thr-arg
UniProt: V5HCK7
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative cathepsin D	protein	339	12% helix, 45% strand	V5HCK7
B	Ala-phe-arg-ile-pro-leu-thr-arg	protein	8	0% helix, 63% strand	—

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.77	0.93	29	empty
2	81	0.53	0.85	17	empty

Interfaces

1 interface between chains.

A–B · 817 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5N70 · Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in complex… · 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 V5HCK7
Elsewhere: RCSB PDB 5N70 · PDBe 5N70 · UniProt V5HCK7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.