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

Crystal structure of unliganded MYORG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 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

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: Q.125, E.127, N.172, T.174, E.175, R.179 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: N.224, V.407, R.410, R.411, Q.430, N.433 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.407 Hydrogen bonds: B:R.411, B:R.411 NAG-NAG.4: 8 residues within 4Å: Chain B: R.82, V.83, R.84, N.162, S.164, E.200, S.202 Ligands: MLI.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.84

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

NAG.5: 2 residues within 4Å: Chain A: N.294, D.297 No protein-ligand interaction detected (PLIP) NAG.6: 8 residues within 4Å: Chain A: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.82 Hydrogen bonds: A:R.82, A:R.84, A:N.162, A:S.164, A:S.202 NAG.7: 2 residues within 4Å: Chain A: R.236, N.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.236 NAG.10: 5 residues within 4Å: Chain B: N.318, Y.319, N.320, G.350, I.351 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.318, B:I.351, B:I.351 NAG.11: 4 residues within 4Å: Chain B: D.237, N.268, A.530, A.534 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.534

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

ACT.8: 7 residues within 4Å: Chain A: 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.12: 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

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

MLI.9: 6 residues within 4Å: Chain A: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG.6 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.82, A:R.204, A:R.204, A:R.221 MLI.13: 6 residues within 4Å: Chain B: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG-NAG.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.162, B:Y.222 Salt bridges: B:R.82, B:R.204, B:R.204, B: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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