SMTL ID : 8awk.1

Structure of recombinant human beta-glucocerebrosidase in complex with D-carbaxylosyl chloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

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

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

SO4.2: 8 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligands: EDO.13, EDO.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Salt bridges: A:R.353 SO4.3: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:K.79, A:K.79, A:R.277, A:R.277, A:R.277, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.7: 6 residues within 4Å: Chain A: G.193, K.194, S.242, G.243, Y.244 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 Water bridges: A:K.194, A:S.242

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

EDO.4: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: R.277, A.302, K.303, Y.304, V.305, H.306 Ligands: EDO.9 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, L.278, Y.304 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: L.296, V.305, H.306, N.333, T.334 Ligands: EDO.5, EDO.22 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.11: 12 residues within 4Å: Chain A: R.2, C.23, D.24, S.25, F.26, L.103, K.106, S.107, S.110, E.112, G.113, K.413 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: R.353, D.358 Ligands: SO4.2 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: V.343, E.349, R.353, S.356, D.358, R.359, Q.362 Ligands: SO4.2 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain A: R.285, V.310, H.311, W.312, D.315, L.324, A.338, S.366, N.370, W.378 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: E.235, S.237, A.238, L.241, Y.244, D.283, Q.284 Ligands: EDO.19 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: N.192, G.193, G.243, Y.244, P.245 Ligands: SO4.7 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: E.235, Y.244, F.246, Q.284, H.311, Y.313, S.345 Ligands: EDO.16, OIW.28 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: L.165, V.172, S.173, L.174, K.224, L.225, Q.226 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490, Y.492 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: L.296, A.302, F.331, P.332, N.333, T.334 Ligands: EDO.9 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: F.37, R.39, S.52, M.53, G.54, P.55, E.481 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: P.71, E.72, P.475, A.476, R.496 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: L.288, P.289, H.290, K.293 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: K.293, T.297, L.330, F.331 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: L.67, L.436, V.437, A.438, N.442, L.444, A.446 Ligand excluded by PLIP

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

NAG.6: 2 residues within 4Å: Chain A: A.58, N.59 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain A: T.138, H.145, N.146 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.146

1 x OIW: (2~{S},3~{S},4~{R})-cyclohex-5-ene-1,2,3,4-tetrol(Covalent)

OIW.28: 15 residues within 4Å: Chain A: C.126, D.127, F.128, W.179, N.234, E.235, F.246, H.311, Y.313, E.340, S.345, W.381, N.396, V.398 Ligands: EDO.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.313, A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:W.381, A:N.396

1 x NA: SODIUM ION(Non-functional Binders)

NA.29: 4 residues within 4Å: Chain A: G.344, S.345, K.346, E.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhosale, S. et al., Single turnover covalent inhibitors for functional chaperoning of lysosomal glycoside hydrolases. To be published

Release Date

2024-03-13

Peptides

Lysosomal acid glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Lysosomal acid glucosylceramidase

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