SMTL ID : 8vli.1

Cryo-EM structure of human HGSNAT bound with CoA and product 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)

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

NAG.2: 3 residues within 4Å: Chain A: A.75, N.162, N.184 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.75 Hydrogen bonds: A:N.162 NAG.3: 3 residues within 4Å: Chain A: W.92, T.93, N.94 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: L.85, N.162, N.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.162, B:N.162, B:N.184 NAG.7: 2 residues within 4Å: Chain B: W.92, N.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.94 NAG.8: 7 residues within 4Å: Chain B: Y.98, F.109, Q.140, N.142, E.147, K.148, E.149 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.98 Hydrogen bonds: B:Q.140, B:Q.140, B:N.142

2 x COA: COENZYME A(Non-covalent)

COA.4: 23 residues within 4Å: Chain A: R.267, L.268, V.271, D.272, R.275, M.282, N.286, F.310, F.313, I.316, M.317, S.320, L.323, S.324, R.345, L.349, V.376, L.380, S.607, I.608, Y.611, K.662 Ligands: 01.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.313, A:L.349, A:L.380, A:I.608, A:Y.611 Hydrogen bonds: A:R.267, A:R.267, A:L.268, A:D.272, A:R.275, A:R.275, A:F.313, A:S.320, A:S.607 Salt bridges: A:R.275, A:R.275, A:R.345, A:R.345, A:K.662 pi-Cation interactions: A:R.267 COA.9: 25 residues within 4Å: Chain B: R.267, L.268, V.271, D.272, R.275, M.282, N.286, F.310, F.313, I.316, M.317, S.320, L.323, S.324, I.328, K.341, R.345, V.376, L.377, L.380, S.607, I.608, Y.611, K.662 Ligands: 01.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.313, B:F.313 Hydrogen bonds: B:L.268, B:D.272, B:R.275, B:S.320, B:S.320, B:S.324 Salt bridges: B:R.275, B:R.275, B:K.341, 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-acetamido-2-deoxy-beta-D-glucopyranoside

01.5: 13 residues within 4Å: Chain A: N.286, Y.287, H.297, A.306, V.309, R.372, V.376, P.498, E.499, K.563, E.615, E.618 Ligands: COA.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.286, A:R.372, A:R.372, A:K.563, A:K.563 Salt bridges: A:H.614 01.10: 12 residues within 4Å: Chain B: V.285, N.286, H.297, A.306, V.309, R.372, V.376, E.499, K.563, E.615, E.618 Ligands: COA.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.285, B:N.286, B:V.309 Hydrogen bonds: B:N.286, B:R.372, B:R.372, B:K.563, B:K.563 Salt bridges: B:H.297

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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