SMTL ID : 8vlg.1

Cryo-EM structure of human HGSNAT bound with Acetyl-CoA and substrate analog

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: 7 residues within 4Å: Chain A: Y.98, F.109, Q.140, N.142, E.147, K.148, E.149 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.162, N.184, E.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.162 NAG.4: 2 residues within 4Å: Chain A: W.92, N.94 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: L.85, N.162, N.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.162 NAG.8: 7 residues within 4Å: Chain B: Y.98, F.109, Q.140, N.142, E.147, K.148, E.149 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.98 Hydrogen bonds: B:Q.140, B:N.142

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 29 residues within 4Å: Chain A: R.267, L.268, R.269, V.271, D.272, R.275, M.282, V.285, N.286, H.297, A.306, V.309, F.310, F.313, I.316, M.317, S.320, L.323, S.324, I.328, R.345, V.376, L.380, K.563, S.607, I.608, Y.611, K.662 Ligands: 01.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.309, A:F.310, A:F.313, A:L.380, A:I.608, A:Y.611 Hydrogen bonds: A:R.267, A:L.268, A:R.269, A:D.272, A:R.275, A:R.275, A:N.286, A:F.313, A:S.320, A:S.324, A:S.607, A:K.662 Salt bridges: A:R.275, A:R.275, A:R.345, A:R.345, A:K.662 pi-Cation interactions: A:R.267 ACO.7: 27 residues within 4Å: Chain B: R.267, L.268, V.271, D.272, R.275, M.282, V.285, N.286, H.297, A.306, V.309, F.310, F.313, I.316, M.317, S.320, L.323, S.324, R.345, V.376, L.380, K.563, S.607, I.608, Y.611, K.662 Ligands: 01.9 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:V.309, B:F.310, B:V.376, B:I.608, B:Y.611 Hydrogen bonds: B:R.267, B:L.268, B:D.272, B:D.272, B:R.275, B:R.275, B:N.286, B:F.313, B:S.320, B:S.324, B:S.324, B:S.607 Salt bridges: B:R.275, B:R.275, B:R.345, B:R.345, B:K.662 pi-Cation interactions: B:R.267

2 x 01: 4-methyl-2-oxo-2H-1-benzopyran-7-yl 2-amino-2-deoxy-beta-D-glucopyranoside

01.5: 11 residues within 4Å: Chain A: N.286, H.297, R.372, V.376, Y.481, P.498, E.499, K.563, E.615, E.618 Ligands: ACO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.372, A:R.372, A:S.485, A:K.563 Salt bridges: A:H.297 01.9: 11 residues within 4Å: Chain B: N.286, H.297, R.372, V.376, Y.481, E.499, K.563, H.614, E.615, E.618 Ligands: ACO.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.618 Hydrogen bonds: B:N.286, B:H.297, B:R.372, B:R.372, B:Y.481, B:K.563 Salt bridges: B:H.297, B:H.614

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, B. et al., Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome. Nat Commun (2024)

Release Date

2024-06-26

Peptides

Heparan-alpha-glucosaminide N-acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Heparan-alpha-glucosaminide N-acetyltransferase

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