MolNFT v1 · #127807 · protein

Crystal structure of cathepsin D zymogen from the tick ixodes ricinus (IRCD1)

5N7N · Putative cathepsin D: “Crystal structure of cathepsin D zymogen from the tick ixodes ricinus (IRCD1)”. X-ray diffraction, 2 ligands (SO4, NH4), 11 pockets (best druggability 0.80). MolNFT v1 #127807 on GenesisL1: 3D structure…

PDB: 5N7N
Type: protein
Length: 1,443 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cathepsin D
UniProt: V5HCK7
Ligands: SO4, NH4
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Putative cathepsin D	protein	361	12% helix, 43% strand	V5HCK7
D	Putative cathepsin D	protein	360	13% helix, 42% strand	V5HCK7

Ligands and binding sites

SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	440	0.80	0.87	68	empty
2	377	0.78	0.88	49	empty
3	1020	0.78	0.80	123	SO4
4	356	0.77	0.87	48	empty
5	446	0.56	0.73	33	SO4

Interfaces

4 interfaces between chains.

A–B · 481 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 367 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 326 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5N7N · Crystal structure of cathepsin D zymogen from the tick ixodes ricinus (IRCD1) · 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 5N7N · PDBe 5N7N · UniProt V5HCK7

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