MolNFT v1 · #113234 · protein

Crystal structure of beta-glucanase SDGLUC5_26A from saccharophagus degradans in complex with tetrasaccharide a, form 1

5A94 · Putative retaining B-glycosidase: “Crystal structure of beta-glucanase SDGLUC5_26A from saccharophagus degradans in complex with tetrasaccharide…”. X-ray diffraction, 3 ligands (BGC, MG, CL), 20 pockets (best druggability 0.65).…

PDB: 5A94
Type: protein
Length: 2,010 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative retaining B-glycosidase
EC: 3.2.1.73
UniProt: Q21KE5
Ligands: BGC, MG, CL
Pockets: 20 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F	Putative retaining B-glycosidase (EC 3.2.1.73)	protein	335	40% helix, 16% strand	Q21KE5
B	Putative retaining B-glycosidase (EC 3.2.1.73)	protein	336	40% helix, 16% strand	Q21KE5
D	Putative retaining B-glycosidase (EC 3.2.1.73)	protein	334	40% helix, 16% strand	Q21KE5

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.65	0.75	56	empty
2	302	0.62	0.79	31	BGC
3	285	0.62	0.79	30	BGC
4	324	0.62	0.78	30	BGC
5	480	0.61	0.75	60	CL

Interfaces

8 interfaces between chains.

D–F · 925 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 916 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 915 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 912 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 908 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5A94 · Crystal structure of beta-Glucanase SdGluc5_26A from Saccharophagus degradans in complex… · the same entry in another collection · chain F against F, 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 Q21KE5
Elsewhere: RCSB PDB 5A94 · PDBe 5A94 · UniProt Q21KE5

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