MolNFT v1 · #14113 · protein

Cathepsin D at pH 7.5

1LYW: “Cathepsin D at pH 7.5”. X-ray diffraction, 17 pockets (best druggability 0.87). MolNFT v1 #14113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1LYW
Type: protein
Length: 1,344 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin D
EC: 3.4.23.5
UniProt: P07339
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Cathepsin D (EC 3.4.23.5)	protein	95	5% helix, 39% strand	P07339
B, D, F, H	Cathepsin D (EC 3.4.23.5)	protein	241	16% helix, 42% strand	P07339

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.87	0.88	90	EPE
2	633	0.66	0.76	55	empty
3	249	0.66	0.83	33	EPE
4	353	0.65	0.80	53	empty
5	176	0.61	0.83	27	EPE

Interfaces

12 interfaces between chains.

C–D · 3296 Å² buried · 69 hydrogen bonds · protein-protein
G–H · 3275 Å² buried · 76 hydrogen bonds · protein-protein
A–B · 3258 Å² buried · 74 hydrogen bonds · protein-protein
E–F · 3171 Å² buried · 76 hydrogen bonds · protein-protein
A–D · 498 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1LYW · Cathepsin D at pH 7.5 · the same entry in another collection · chain H against H, TM-score 1.00
P07339 · AlphaFold monomer V2.0 prediction for cathepsin D (P07339) · a predicted model of the same protein · chain H against A, TM-score 0.93

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 P07339
Elsewhere: RCSB PDB 1LYW · PDBe 1LYW · UniProt P07339

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