SMTL ID : 7qqg.1 (1 other biounit)

Crystal structure of MYORG bound to 1-deoxygalactonojirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

2 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: 4 residues within 4Å: Chain A: Q.125, N.172, T.174, E.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.224, R.410, R.411, Q.430, N.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.411, A:R.411

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: E.233, R.236, D.237, N.268, A.534 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.236, A:E.233, A:R.236, A:R.236

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

NAG.4: 8 residues within 4Å: Chain A: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.68 Hydrogen bonds: A:R.82, A:R.84, A:N.162, A:S.164, A:S.202 NAG.5: 2 residues within 4Å: Chain A: P.293, N.294 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: P.280, A.281, N.320 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.281 Hydrogen bonds: A:P.280, A:N.320 NAG.10: 3 residues within 4Å: Chain B: R.236, N.268, A.534 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.236, B:R.236, B:D.237 NAG.11: 6 residues within 4Å: Chain A: E.329 Chain B: N.318, Y.319, N.320, G.350, I.351 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.320, B:I.351, B:I.351

2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.6: 11 residues within 4Å: Chain A: W.243, D.275, D.276, W.312, W.348, K.383, D.385, R.426, R.439, D.442, M.475 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.276, A:D.276, A:W.348, A:K.383, A:K.383, A:D.385, A:D.385, A:R.426, A:R.439, A:R.439, A:D.442 DGJ.9: 10 residues within 4Å: Chain B: W.243, D.275, D.276, W.312, W.348, K.383, D.385, R.426, R.439, D.442 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.276, B:W.348, B:K.383, B:K.383, B:D.385, B:R.426, B:R.439, B:R.439, B:D.442

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.7: 6 residues within 4Å: Chain A: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG.4 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.162, A:R.204 Salt bridges: A:R.82, A:R.204, A:R.204, A:R.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meek, R.W. et al., The primary familial brain calcification-associated protein MYORG is an alpha-galactosidase with restricted substrate specificity. Plos Biol. (2022)

Release Date

2022-08-31

Peptides

Myogenesis-regulating glycosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Myogenesis-regulating glycosidase

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