Research workbench

Crystal structure of DEG5

Analyse Crystal structure of DEG5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IC5
Type: protein
Length: 629 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease do-like 5, chloroplastic
EC: 3.4.21.-
UniProt: Q9SEL7
Ligands: CA
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease do-like 5, chloroplastic (EC 3.4.21.-)	protein	210	21% helix, 34% strand	Q9SEL7
C	Protease do-like 5, chloroplastic (EC 3.4.21.-)	protein	209	18% helix, 34% strand	Q9SEL7

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.82	0.90	52	CA
2	113	0.47	0.79	15	empty
3	99	0.45	0.79	14	empty
4	99	0.44	0.78	16	empty
5	70	0.36	0.78	15	empty

Interfaces

3 interfaces between chains.

B–C · 912 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 909 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 908 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4IC5 · Crystal structure of Deg5 · the same entry in another collection · chain A against A, TM-score 1.00
Q9SEL7 · AlphaFold monomer V2.0 prediction for protease do-like 5, chloroplastic (Q9SEL7) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9SEL7
Elsewhere: RCSB PDB 4IC5 · PDBe 4IC5 · UniProt Q9SEL7

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