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Structure of human sialyltransferase ST8SIAIII

Analyse Structure of human sialyltransferase ST8SIAIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BO8
Type: protein
Length: 553 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase
EC: 2.4.99.-
UniProt: O43173
Ligands: NAG, BMA, MAN, FUC
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase (EC 2.4.99.-)	protein	277	41% helix, 14% strand	O43173
B	Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase (EC 2.4.99.-)	protein	276	41% helix, 14% strand	O43173

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains B
CIT · Citric acid · additive · chains B

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

Pockets

8 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	522	0.71	0.80	51	empty
2	437	0.67	0.79	41	empty
3	62	0.57	0.90	18	empty
4	127	0.44	0.77	18	empty
5	110	0.44	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 1031 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

5BO8 · Structure of human sialyltransferase ST8SiaIII · the same entry in another collection · chain A against A, TM-score 1.00
O43173 · AlphaFold monomer V2.0 prediction for sia-alpha-2,3-gal- beta-1,4-glcnac-R:ALPHA… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O43173
Elsewhere: RCSB PDB 5BO8 · PDBe 5BO8 · UniProt O43173

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