SMTL ID : 9h6l.1

Human B4GALNT1 in Complex with UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.240, A.243, T.271, Y.290 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.290 Hydrogen bonds: A:Y.290 NAG-NAG-BMA.2: 4 residues within 4Å: Chain B: G.231, N.240, A.243, Y.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.290

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

UDP.3: 12 residues within 4Å: Chain A: R.254, W.302, D.322, D.324, N.403, R.423, V.424, A.425, H.426, H.449, R.471 Ligands: MN.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.403, A:R.423, A:A.425, A:A.425, A:H.426 Salt bridges: A:R.254, A:H.449, A:R.471 pi-Stacking: A:W.302, A:W.302 UDP.6: 12 residues within 4Å: Chain B: R.254, W.302, D.322, D.324, N.403, R.423, V.424, A.425, H.426, H.449, Y.472 Ligands: MN.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.322, B:N.403, B:R.423, B:A.425, B:A.425, B:H.426 Salt bridges: B:R.254, B:H.449 pi-Stacking: B:W.302, B:W.302

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

MN.4: 3 residues within 4Å: Chain A: D.324, H.449 Ligands: UDP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.324, A:D.324, A:H.449 MN.7: 3 residues within 4Å: Chain B: D.324, H.449 Ligands: UDP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.324, B:H.449

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

ACY.5: 7 residues within 4Å: Chain A: R.226, D.410, R.413 Chain B: R.413, E.414, V.415, G.416 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.410 Salt bridges: A:R.226, A:R.413 ACY.8: 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 Hydrogen bonds: B:D.410 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

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