SMTL ID : 6tjj.1 (1 other biounit)

Structure of Cerezyme at pH 4.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:W.357, A:D.358 Salt bridges: A:R.353 SO4.3: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.45 Salt bridges: A:R.44 SO4.4: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:K.79, A:K.79, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.5: 2 residues within 4Å: Chain A: E.254, R.257 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.254, A:E.254 Salt bridges: A:R.257 SO4.6: 2 residues within 4Å: Chain A: R.329, L.330 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.329 SO4.7: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.44 SO4.8: 2 residues within 4Å: Chain A: K.473, P.475 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.473 SO4.9: 3 residues within 4Å: Chain A: E.111, R.170, P.428 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.170 SO4.12: 3 residues within 4Å: Chain A: P.289, H.290, K.293 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.290, A:K.293 Salt bridges: A:H.290, A:K.293 SO4.14: 2 residues within 4Å: Chain A: A.1, R.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.1, A:R.2 SO4.19: 3 residues within 4Å: Chain A: S.465, K.466, D.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.467, A:D.467

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

ACT.10: 2 residues within 4Å: Chain A: K.7, S.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.7 Hydrogen bonds: A:S.8 Salt bridges: A:K.7 ACT.11: 3 residues within 4Å: Chain A: R.131, P.150, E.151 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.150 Hydrogen bonds: A:E.151 Salt bridges: A:R.131 ACT.13: 5 residues within 4Å: Chain A: R.277, K.303, Y.304, V.305, H.306 5 PLIP interactions: 5 interactions with chain A Water bridges: A:V.305, A:V.305, A:H.306 Salt bridges: A:R.277, A:H.306 ACT.15: 2 residues within 4Å: Chain A: Q.57, A.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.58 ACT.16: 3 residues within 4Å: Chain A: T.43, S.45, R.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.45 Salt bridges: A:R.47 ACT.17: 3 residues within 4Å: Chain A: T.187, K.198, G.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.199 Salt bridges: A:K.198 ACT.18: 5 residues within 4Å: Chain A: Q.226, T.272, H.273, N.275, V.276 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.275 Salt bridges: A:H.273

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

NAG.20: 4 residues within 4Å: Chain A: T.138, D.141, H.145, N.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rowland, R.J. et al., A baculoviral system for the production of human beta-glucocerebrosidase enables atomic resolution analysis. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-06-10

Peptides

Glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Glucosylceramidase

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