SMTL ID : 7qqf.2 (1 other biounit)

Crystal structure of unliganded MYORG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

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: 4 residues within 4Å: Chain A: Q.125, N.172, E.175, R.179 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.84 NAG-NAG.5: 5 residues within 4Å: Chain B: N.224, R.410, R.411, Q.430, N.433 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.411, B:R.411 NAG-NAG.6: 4 residues within 4Å: Chain B: Q.125, N.172, E.175, R.179 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.224, R.410, R.411, Q.430, N.433 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.410 Hydrogen bonds: A:R.411, A:R.411

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.4: 2 residues within 4Å: Chain B: N.294, D.297 No protein-ligand interaction detected (PLIP)

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

NAG.7: 7 residues within 4Å: Chain A: P.280, N.318, Y.319, N.320, G.350, I.351 Chain B: E.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.351, A:I.351 NAG.8: 4 residues within 4Å: Chain A: R.236, D.237, N.268, A.534 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.236, A:D.237, A:N.268 NAG.9: 1 residues within 4Å: Chain A: N.294 No protein-ligand interaction detected (PLIP) NAG.12: 8 residues within 4Å: Chain B: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.68, B:R.82 Hydrogen bonds: B:R.82, B:R.84, B:S.164, B:S.202 NAG.13: 6 residues within 4Å: Chain A: E.329 Chain B: N.318, Y.319, N.320, G.350, I.351 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.351, B:I.351 NAG.14: 5 residues within 4Å: Chain B: R.236, D.237, N.268, A.530, A.534 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.236, B:N.268

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

MLI.10: 6 residues within 4Å: Chain A: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG-NAG.2 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 MLI.15: 6 residues within 4Å: Chain B: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.222 Salt bridges: B:R.82, B:R.204, B:R.204, B:R.221

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 8 residues within 4Å: Chain A: G.109, G.110, A.111, M.113, I.120, F.143, W.151, L.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.111 ACT.16: 5 residues within 4Å: Chain B: G.110, A.111, M.113, I.120, W.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.111

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
B

B
C

Myogenesis-regulating glycosidase

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