SMTL ID : 9h6k.1

Human B4GALNT1 in Complex with UDP-GalNac

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 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: G.231, N.240, S.242, A.243, Y.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.290 NAG-NAG.2: 4 residues within 4Å: Chain B: G.231, N.240, A.243, Y.290 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.290 Hydrogen bonds: B:Y.290

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

NAG.3: 3 residues within 4Å: Chain A: N.145, S.207, T.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.145, A:S.207 NAG.4: 2 residues within 4Å: Chain A: W.43, N.45 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain B: Q.143, N.145, T.173, S.207, T.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.173 NAG.9: 2 residues within 4Å: Chain B: W.43, N.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.45

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

MN.5: 3 residues within 4Å: Chain A: D.324, H.449 Ligands: UD2.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.324, A:D.324, A:H.449 MN.10: 3 residues within 4Å: Chain B: D.324, H.449 Ligands: UD2.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.324, B:H.449, H2O.2

2 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.6: 21 residues within 4Å: Chain A: K.250, T.251, F.252, R.254, W.302, D.322, D.323, D.324, F.325, V.402, N.403, S.422, R.423, V.424, A.425, H.426, H.449, Y.467, Y.470, R.471 Ligands: MN.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.325, A:V.402 Hydrogen bonds: A:K.250, A:K.250, A:R.254, A:D.322, A:D.322, A:D.322, A:D.323, A:D.323, A:N.403, A:N.403, A:R.423, A:A.425, A:H.426, A:Y.467 Water bridges: A:K.250, A:T.251, A:D.279 Salt bridges: A:R.254, A:H.449, A:R.471, A:R.471, A:R.471 UD2.11: 20 residues within 4Å: Chain B: K.250, T.251, F.252, R.254, W.302, D.322, D.323, D.324, F.325, V.402, N.403, R.423, V.424, A.425, H.426, H.449, Y.467, Y.470, R.471 Ligands: MN.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.325, B:V.402 Hydrogen bonds: B:K.250, B:K.250, B:F.252, B:R.254, B:D.322, B:D.322, B:D.323, B:D.323, B:N.403, B:N.403, B:R.423, B:R.423, B:A.425, B:H.426, B:Y.467 Salt bridges: B:R.254, B:R.471, B:R.471, B:R.471

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 6 residues within 4Å: Chain A: D.410, R.413 Chain B: R.413, E.414, V.415, G.416 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.226, A:R.413 ACY.12: 7 residues within 4Å: Chain A: R.413, E.414, V.415, G.416 Chain B: R.226, D.410, R.413 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.410, B:R.413 Salt bridges: B:R.226, B:R.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welland, J.W.J. et al., Conformational dynamics and membrane insertion mechanism of B4GALNT1 in ganglioside synthesis. Nat Commun (2025)

Release Date

2025-07-16

Peptides

Beta-1,4 N-acetylgalactosaminyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-1,4 N-acetylgalactosaminyltransferase 1

Related Entries With Identical Sequence