SMTL ID : 8zwy.1 (1 other biounit)

Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 7 residues within 4Å: Chain A: D.93, F.94, L.95, V.97, Y.99, N.100, L.103 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 3 residues within 4Å: Chain A: K.142, K.143, N.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.142, A:N.144

1 x MBG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-methyl beta-D-galactopyranoside(Non-covalent)

MBG-NAG.3: 12 residues within 4Å: Chain A: K.155, E.158, I.161, W.168, Y.180, F.183, S.185, T.187, L.211, D.213, V.214, P.238 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.155, A:G.186, A:G.186, A:F.159 Hydrogen bonds: A:K.155, A:E.158 Salt bridges: A:K.155

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

MN.4: 4 residues within 4Å: Chain A: D.126, D.128, H.255 Ligands: UDP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.126, A:D.128, A:D.128, A:H.255

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.5: 16 residues within 4Å: Chain A: T.34, S.35, S.36, Q.39, D.96, V.97, Y.98, L.101, K.104, D.126, S.127, D.128, K.167, W.168, H.255 Ligands: MN.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.34, A:T.34, A:S.36, A:Q.39, A:Q.39, A:D.96, A:D.96, A:Y.98, A:S.127, A:S.127 Water bridges: A:V.97, A:Y.98, A:D.126, A:D.128 Salt bridges: A:K.167, A:K.167, A:H.255

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

B3P.6: 9 residues within 4Å: Chain A: Y.175, W.177, R.179, Y.180, P.181, P.207, L.218, E.221, R.222 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.177 Hydrogen bonds: A:R.179, A:E.221, A:E.221, A:R.222

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
A

Beta-1,3-galactosyltransferase 5

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