MolNFT v1 · #123894 · protein

DEG9 crystal under 289K

5JYK · Protease do-like 9: “DEG9 crystal under 289K”. X-ray diffraction, 9 pockets (best druggability 0.70). MolNFT v1 #123894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JYK
Type: protein
Length: 877 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease do-like 9
EC: 3.4.21.-
UniProt: Q9FL12
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease do-like 9 (EC 3.4.21.-)	protein	465	20% helix, 37% strand	Q9FL12
B	Protease do-like 9 (EC 3.4.21.-)	protein	412	21% helix, 32% strand	Q9FL12

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.70	0.77	76	empty
2	651	0.67	0.76	77	empty
3	474	0.67	0.78	45	GOL
4	121	0.50	0.80	20	empty
5	58	0.41	0.81	13	empty

Interfaces

1 interface between chains.

A–B · 1528 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5JYK · Deg9 crystal under 289K · the same entry in another collection · chain A against A, TM-score 1.00
Q9FL12 · AlphaFold monomer V2.0 prediction for protease do-like 9 (Q9FL12) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9FL12
Elsewhere: RCSB PDB 5JYK · PDBe 5JYK · UniProt Q9FL12

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