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

Crystal structure of MYORG (D520N) in complex with Gal-a1,4-Glc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

5 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: 5 residues within 4Å: Chain A: N.224, R.410, R.411, Q.430, N.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.411, A:R.411 Water bridges: A:Q.430 NAG-NAG.2: 5 residues within 4Å: Chain A: Q.125, E.127, N.172, E.175, R.179 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.318, Y.319, N.320, G.350, I.351 Chain B: E.329 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.351, B:E.329, B:E.329 NAG-NAG.4: 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.5: 5 residues within 4Å: Chain B: Q.125, E.127, N.172, E.175, R.179 No protein-ligand interaction detected (PLIP)

2 x BGC- GLA: alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GLA.6: 15 residues within 4Å: Chain A: D.135, Y.137, W.243, R.248, D.275, D.276, W.312, W.348, K.383, D.385, Y.391, R.426, R.439, N.442, M.475 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.135, A:D.135, A:Y.391, A:R.426, A:R.426, A:N.442, A:R.248, A:D.276, A:D.276, A:N.349, A:K.383, A:K.383, A:D.385, A:R.426, A:R.439, A:R.439, A:N.442 Water bridges: A:D.135, A:S.138, A:N.442, A:D.474 BGC-GLA.7: 15 residues within 4Å: Chain B: D.135, Y.137, W.243, R.248, D.275, D.276, W.312, W.348, K.383, D.385, Y.391, R.426, R.439, N.442, M.475 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.135, B:D.135, B:R.248, B:R.426, B:R.426, B:N.442, B:R.248, B:D.276, B:K.383, B:K.383, B:D.385, B:R.426, B:R.439, B:R.439, B:N.442 Water bridges: B:D.135, B:S.138, B:N.442, B:D.474

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

NAG.8: 8 residues within 4Å: Chain A: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.12 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.9: 4 residues within 4Å: Chain A: R.236, D.237, N.268, A.534 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.534 Hydrogen bonds: A:R.236, A:N.268 NAG.13: 8 residues within 4Å: Chain B: F.68, R.82, V.83, R.84, N.162, S.164, S.202 Ligands: MLI.17 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.68, B:R.82 Hydrogen bonds: B:R.82, B:R.84, B:N.162, B:S.164, B:S.202 NAG.14: 4 residues within 4Å: Chain B: R.236, D.237, N.268, A.534 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.236, B:D.237, B:N.268 NAG.15: 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

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 6 residues within 4Å: Chain A: I.239, H.271, L.422, A.423, E.424, L.472 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.422 EDO.11: 7 residues within 4Å: Chain A: G.109, G.110, A.111, M.113, I.120, W.151, L.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.111 EDO.16: 8 residues within 4Å: Chain B: G.110, A.111, M.113, I.120, L.122, F.143, W.151, L.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.111 EDO.18: 6 residues within 4Å: Chain B: I.239, H.271, L.422, A.423, E.424, L.472 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.422 Water bridges: B:E.424

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

MLI.12: 6 residues within 4Å: Chain A: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG.8 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.82, A:R.204, A:R.204, A:R.221 MLI.17: 6 residues within 4Å: Chain B: R.82, N.162, R.204, R.221, Y.222 Ligands: NAG.13 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

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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