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Structure of inactive mutant of strictosidine glucosidase in complex with strictosidine

Analyse Structure of inactive mutant of strictosidine glucosidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JF6
Type: protein
Length: 936 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Strictosidine-O-beta-D-glucosidase
EC: 3.2.1.105
UniProt: Q8GU20
Ligands: S55
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Strictosidine-O-beta-D-glucosidase (EC 3.2.1.105)	protein	464	45% helix, 17% strand	Q8GU20
B	Strictosidine-O-beta-D-glucosidase (EC 3.2.1.105)	protein	472	45% helix, 17% strand	Q8GU20

Ligands and binding sites

S55 · Methyl (2S,3R,4S)-3-ethyl-2-(beta-D-glucopyranosyloxy)-4-[(1S)-2,3,4,9-tetrahydro-1H-beta-carbolin-1-ylmethyl]-3,4-dihydro-2H-pyran-5-carboxylate · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	231	0.81	0.94	44	empty
2	451	0.72	0.81	44	S55
3	405	0.71	0.82	42	S55
4	150	0.44	0.75	18	empty
5	141	0.42	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 656 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2JF6 · Structure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine · the same entry in another collection · chain A against A, TM-score 1.00
Q8GU20 · AlphaFold monomer V2.0 prediction for strictosidine-O-beta-D- glucosidase (Q8GU20) · a predicted model of the same protein · 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 Q8GU20
Elsewhere: RCSB PDB 2JF6 · PDBe 2JF6 · UniProt Q8GU20

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