MolNFT v1 · #128102 · protein

The endo-BETA1,6-glucanase BT3312

5NGK · Glucosylceramidase: “The endo-BETA1,6-glucanase BT3312”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #128102 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NGK
Type: protein
Length: 1,367 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosylceramidase
UniProt: A0A173SYZ2
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosylceramidase	protein	458	30% helix, 28% strand	A0A173SYZ2
B	Glucosylceramidase	protein	455	30% helix, 28% strand	A0A173SYZ2
C	Glucosylceramidase	protein	454	30% helix, 28% strand	A0A173SYZ2

Pockets

9 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	804	0.74	0.79	84	empty
2	784	0.71	0.77	83	empty
3	414	0.55	0.73	47	empty
4	72	0.36	0.77	19	empty
5	89	0.34	0.74	17	empty

Interfaces

3 interfaces between chains.

B–C · 456 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 444 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 288 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5NGK · The endo-beta1,6-glucanase BT3312 · the same entry in another collection · 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 A0A173SYZ2
Elsewhere: RCSB PDB 5NGK · PDBe 5NGK · UniProt A0A173SYZ2

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