MolNFT v1 · #94963 · protein

Crystal structure of DEG8

4IC6 · Protease do-like 8, chloroplastic: “Crystal structure of DEG8”. X-ray diffraction, 11 pockets (best druggability 0.87). MolNFT v1 #94963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4IC6
Type: protein
Length: 1,014 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease do-like 8, chloroplastic
EC: 3.4.21.-
UniProt: Q9LU10
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease do-like 8, chloroplastic (EC 3.4.21.-)	protein	340	17% helix, 37% strand	Q9LU10
B	Protease do-like 8, chloroplastic (EC 3.4.21.-)	protein	339	18% helix, 37% strand	Q9LU10
C	Protease do-like 8, chloroplastic (EC 3.4.21.-)	protein	335	19% helix, 36% strand	Q9LU10

Pockets

11 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	835	0.87	0.89	116	empty
2	273	0.76	0.89	47	empty
3	358	0.72	0.84	51	empty
4	115	0.60	0.86	25	empty
5	128	0.58	0.84	32	empty

Interfaces

3 interfaces between chains.

B–C · 1627 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1432 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1191 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4IC6 · Crystal structure of Deg8 · the same entry in another collection · chain A against A, TM-score 1.00
Q9LU10 · AlphaFold monomer V2.0 prediction for protease do-like 8, chloroplastic (Q9LU10) · a predicted model of the same protein · chain B against A, TM-score 0.82

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 Q9LU10
Elsewhere: RCSB PDB 4IC6 · PDBe 4IC6 · UniProt Q9LU10

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