SMTL ID : 9bgf.1

Structure of human GlcNAc-1-phosphotransferase complexed with the donor substrate UDP-GlcNAc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

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: 9 residues within 4Å: Chain B: W.51, N.53, G.54, T.55, D.56, D.295, P.325, S.326, W.327 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.988, D.990, S.992, V.994, S.996, E.999 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.988, A:S.992, A:V.994, A:E.999, A:E.999 CA.14: 6 residues within 4Å: Chain B: D.988, D.990, S.992, V.994, S.996, E.999 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.990, B:D.990, B:S.992, B:V.994, B:E.999

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.291, E.294 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: N.376, D.378, N.1121 Ligands: UD1.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.378 MG.11: 4 residues within 4Å: Chain B: N.376, D.378, N.1121 Ligands: UD1.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.378 MG.15: 3 residues within 4Å: Chain B: S.291, E.294, D.378 No protein-ligand interaction detected (PLIP)

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.4: 23 residues within 4Å: Chain A: T.50, W.51, V.52, R.292, F.293, F.353, S.354, S.355, P.356, I.358, E.359, Y.374, N.376, D.377, D.378, F.901, H.926, M.927, H.929, R.956, Q.962, N.1121 Ligands: MG.9 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.52, A:N.376 Hydrogen bonds: A:T.50, A:V.52, A:E.359, A:N.376, A:N.376, A:N.376, A:D.377, A:D.377, A:Q.962, A:N.1121 Salt bridges: A:R.292, A:R.292, A:H.926, A:R.956, A:R.956, A:R.956 UD1.12: 22 residues within 4Å: Chain B: T.50, W.51, V.52, R.292, F.293, F.353, S.354, S.355, P.356, I.358, E.359, N.376, D.377, D.378, F.901, H.926, M.927, H.929, R.956, Q.962, N.1121 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.52, B:F.293, B:N.376 Hydrogen bonds: B:T.50, B:V.52, B:S.355, B:E.359, B:N.376, B:N.376, B:N.376, B:D.377, B:Q.962, B:N.1121 Salt bridges: B:R.292, B:R.292, B:H.926, B:R.956, B:R.956, B:R.956

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

NAG.5: 1 residues within 4Å: Chain A: N.1099 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: N.346, S.348, H.349, D.948 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.348 NAG.7: 9 residues within 4Å: Chain A: W.51, N.53, T.55, D.295, I.324, P.325, S.326, W.327, L.1163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.53, A:S.326, A:S.326, A:S.326 NAG.8: 2 residues within 4Å: Chain A: N.979, S.981 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain B: N.1099, S.1101, H.1102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1099 NAG.13: 3 residues within 4Å: Chain B: N.346, S.348, H.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structure of a truncated human GlcNAc-1-phosphotransferase variant reveals the basis for its hyperactivity. J.Biol.Chem. (2024)

Release Date

2025-02-26

Peptides

N-acetylglucosamine-1-phosphotransferase subunits alpha/beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-1-phosphotransferase subunits alpha/beta

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