SMTL ID : 8awr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 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: 3 residues within 4Å: Chain A: I.5, N.19, T.21 No protein-ligand interaction detected (PLIP)

2 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:R.353, A:S.356 Salt bridges: A:R.353 SO4.3: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.79, A:K.79 Salt bridges: A:K.79, A:R.277, A:H.306

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

EDO.4: 6 residues within 4Å: Chain A: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: F.37, R.39, M.53, G.54, E.481 Ligands: OIZ.24 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: E.235, S.237, A.238, L.241, Y.244, D.283, Q.284 Ligands: EDO.17 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: P.289, H.290, K.293 Ligands: EDO.22 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, Y.304 Ligand excluded by PLIP EDO.10: 10 residues within 4Å: Chain A: R.2, C.23, D.24, S.25, L.103, K.106, S.107, E.112, G.113, K.413 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: T.369, L.372, D.445 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: L.165, V.172, L.174, L.225, Q.226 Ligands: EDO.27 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: R.277, A.302, K.303, V.305 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: R.285, V.310, H.311, W.312, D.315, L.324, A.338, S.366, N.370 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: E.235, Y.244, Q.284, Y.313, S.345 Ligands: EDO.6, OJ6.25 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: K.74, Q.432 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: F.75, L.372, R.433 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: L.67, L.436, A.438, N.442, L.444 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: K.106, S.110, E.112, L.167, Q.169 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: K.293, V.294 Ligands: EDO.8 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: W.312, Y.313, D.315, F.316, K.346 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: A.221, K.224, L.225, Q.226 Ligands: EDO.13 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: R.131, Y.133, T.134, P.150 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: S.148, L.149, T.154 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: F.347, W.348, E.349, Q.350 Ligand excluded by PLIP

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

NAG.11: 1 residues within 4Å: Chain A: N.59 No protein-ligand interaction detected (PLIP) NAG.26: 3 residues within 4Å: Chain A: T.138, H.145, N.146 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.138 Water bridges: A:N.146

1 x OIZ: (1~{S},2~{R},3~{S},6~{S})-6-chloranylcyclohex-4-ene-1,2,3-triol(Non-covalent)

OIZ.24: 9 residues within 4Å: Chain A: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.47 Water bridges: A:E.41 Halogen bonds: A:T.482, A:I.483

1 x OJ6: (1~{S},2~{S},3~{S},4~{R})-cyclohexane-1,2,3,4-tetrol(Covalent)

OJ6.25: 11 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, W.381, N.396 Ligands: EDO.17 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:E.235, A:N.396

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.31: 2 residues within 4Å: Chain A: E.254, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.257, A:R.257 Water bridges: A:E.254, A:D.258

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

NA.32: 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 NA.33: 2 residues within 4Å: Chain A: L.165, A.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.165

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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