SMTL ID : 7s05.1

Cryo-EM structure of human GlcNAc-1-phosphotransferase A2B2 subcomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 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: 6 residues within 4Å: Chain A: W.51, N.53, G.54, T.55, S.326, W.327 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.1099, S.1101, H.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: W.51, N.53, G.54, T.55, S.326, W.327 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.1099, S.1101, H.1102 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: N.979, S.981, Q.982, D.985 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.982 Hydrogen bonds: A:Q.982 NAG.6: 2 residues within 4Å: Chain A: H.1022, N.1026 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: N.346, S.348, H.349, F.952 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain B: N.979, S.981, Q.982, D.985 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.982 Hydrogen bonds: B:Q.982 NAG.10: 2 residues within 4Å: Chain B: H.1022, N.1026 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain B: N.346, S.348, H.349, F.952 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.988, D.990, S.992, V.994, E.999 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.988, A:D.990, A:V.994, A:E.999 CA.12: 5 residues within 4Å: Chain B: D.988, D.990, S.992, V.994, E.999 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.988, B:D.990, B:V.994, B:E.999

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structure of the human GlcNAc-1-phosphotransferase alpha beta subunits reveals regulatory mechanism for lysosomal enzyme glycan phosphorylation. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-03-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

N-acetylglucosamine-1-phosphotransferase subunits alpha/beta

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