SMTL ID : 8zx2.2 (1 other biounit)

Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: F.94, L.95, V.97, Y.99, N.100 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 1 residues within 4Å: Chain A: N.144 No protein-ligand interaction detected (PLIP)

1 x BMA- MAN- GAL: beta-D-galactopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose

BMA-MAN-GAL.3: 16 residues within 4Å: Chain A: Y.98, L.101, K.124, D.126, K.155, E.158, I.161, W.168, Y.180, F.183, S.185, G.186, T.187, L.211, E.212, D.213 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.155, A:K.155, A:K.155, A:D.213, A:K.124, A:K.124, A:D.126, A:S.185, A:G.186, A:T.187, A:K.210, A:E.212, A:E.212 Salt bridges: A:K.155 Water bridges: A:E.158, A:G.186, A:G.186

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 3 residues within 4Å: Chain A: D.126, D.128, H.255 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.128, A:D.128, A:H.255, H2O.1

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.5: 10 residues within 4Å: Chain A: Y.175, W.177, R.179, Y.180, P.181, P.182, P.207, L.218, E.221, R.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.177 Hydrogen bonds: A:E.221, A:E.221, A:E.221

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 1 residues within 4Å: Chain A: N.201 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lo, J.M. et al., Structure-Based Mechanism and Specificity of Human Galactosyltransferase beta 3GalT5. J.Am.Chem.Soc. (2025)

Release Date

2025-04-09

Peptides

Beta-1,3-galactosyltransferase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-1,3-galactosyltransferase 5

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