SMTL ID : 8ax3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: R.2, I.5, N.19, A.20, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: I.5, N.19, A.20, T.21, Y.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.5

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.3: 1 residues within 4Å: Chain B: N.59 No protein-ligand interaction detected (PLIP)

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

SO4.4: 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:W.357, A:D.358 Water bridges: A:R.353 Salt bridges: A:R.353 SO4.5: 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 SO4.16: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.44 Salt bridges: A:R.44 SO4.34: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:S.356, B:W.357, B:D.358 Water bridges: B:S.12, B:R.353, B:R.359 Salt bridges: B:R.353 SO4.37: 5 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligands: EDO.60 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.228 Water bridges: B:K.79, B:K.79, B:R.277, B:R.277, B:H.306, B:E.429 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.47: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.44

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

EDO.6: 8 residues within 4Å: Chain A: P.3, C.4, D.24, G.46, R.47, R.48, E.50 Ligands: EDO.29 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: F.75, L.372, Y.373, H.374, R.433 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: L.91, N.92, A.95, N.386, P.391, I.406 Ligand excluded by PLIP EDO.9: 10 residues within 4Å: Chain A: W.312, Y.313, C.342, V.343, G.344, S.345, K.346, E.349, Q.362 Chain B: L.241 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: E.254, R.257 Ligands: EDO.26 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.305, H.306, N.333, T.334 Ligands: EDO.12, EDO.14 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: R.277, A.302, K.303, Y.304, V.305, H.306 Ligands: EDO.11, EDO.30 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: L.296, A.302, F.331, P.332, N.333, T.334 Ligands: EDO.11 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: V.343, W.348, E.349, Q.350, R.353, R.359 Chain B: S.242, G.243 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: L.165, A.168, Q.169, R.170, P.171, V.172 Ligand excluded by PLIP EDO.19: 11 residues within 4Å: Chain A: R.285, V.310, H.311, W.312, D.315, L.324, A.338, S.366, N.370, V.375, W.378 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: K.321, A.322, G.325, E.326, R.329 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284, L.314 Chain B: F.316, L.317 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: D.467, I.483 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: S.196, G.199, Q.200, P.201, H.255 Ligands: EDO.26, EDO.27 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: Q.200, P.201, T.252, E.254, H.255, D.258 Ligands: EDO.10, EDO.25, EDO.27 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: T.252, E.254, H.255 Ligands: EDO.25, EDO.26 Ligand excluded by PLIP EDO.28: 10 residues within 4Å: Chain A: F.109, S.110, E.111, G.115, Y.116, N.117, A.168, Q.169, R.170, V.172 Ligand excluded by PLIP EDO.29: 11 residues within 4Å: Chain A: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, Y.418 Ligands: EDO.6 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligands: EDO.12 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: H.162, L.165, Q.166, K.224, L.225 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain A: L.286, L.317, A.318, P.319, T.323 Chain B: L.286, L.287, H.290, W.291 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP EDO.36: 11 residues within 4Å: Chain B: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, F.417, Y.418 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain A: S.242, G.243 Chain B: V.343, W.348, E.349, Q.350, R.353, R.359 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain B: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain B: F.37, R.39, S.52, M.53, G.54, P.55, E.481 Ligands: OD0.48 Ligand excluded by PLIP EDO.42: 10 residues within 4Å: Chain A: F.316, L.317 Chain B: E.235, S.237, A.238, Y.244, D.283, Q.284, L.314 Ligands: CA.65 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP EDO.44: 12 residues within 4Å: Chain B: C.23, D.24, S.25, F.26, L.103, K.106, S.107, S.110, E.112, G.113, K.413 Ligands: EDO.61 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain B: L.91, N.92, A.95, N.386, P.391, I.406 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: F.9, L.354, P.387, D.405, K.408, Y.412 Ligand excluded by PLIP EDO.51: 8 residues within 4Å: Chain B: E.111, R.170, K.425, F.426, I.427, P.428, H.451 Ligands: EDO.52 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain B: P.29, Y.40, E.111, R.170, K.425, F.426 Ligands: EDO.51 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain B: D.453, G.454, S.455, R.495, R.496, Q.497 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain B: N.102, L.105, R.163, Q.166, L.167 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain B: T.132, Y.133, T.134, D.137, T.183, V.191 Ligands: GOL.55 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain B: R.277, A.302, K.303, Y.304, V.305, H.306 Ligand excluded by PLIP EDO.58: 10 residues within 4Å: Chain A: L.241 Chain B: W.312, Y.313, C.342, V.343, G.344, S.345, K.346, E.349, Q.362 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain B: Q.70, P.71, E.72, Q.73 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain B: K.79, E.429 Ligands: SO4.37 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain B: R.2, C.23, D.24, S.25, L.103 Ligands: EDO.44 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain B: F.31, H.451, D.453, S.455, L.493, R.495 Ligand excluded by PLIP EDO.63: 8 residues within 4Å: Chain B: K.77, G.430, S.431, Q.432, M.450, H.451, P.452, G.454 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain B: F.75, L.372, Y.373, H.374, R.433 Ligand excluded by PLIP

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

NAG.13: 3 residues within 4Å: Chain A: T.138, H.145, N.146 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.138 NAG.46: 3 residues within 4Å: Chain B: T.138, H.145, N.146 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.146, B:N.146

4 x OD0: (1~{S},2~{R},3~{S},6~{S})-6-fluoranylcyclohex-4-ene-1,2,3-triol(Non-covalent)

OD0.18: 9 residues within 4Å: Chain A: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490, Y.492 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.41, A:R.47 Water bridges: A:E.41 Halogen bonds: A:T.482, A:I.483 OD0.21: 17 residues within 4Å: Chain A: R.120, C.126, D.127, F.128, W.179, N.234, E.235, F.246, H.311, Y.313, E.340, C.342, S.345, W.381, N.382, N.396, V.398 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.313 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.340, A:W.381, A:N.396 OD0.48: 10 residues within 4Å: Chain B: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490, Y.492 Ligands: EDO.41 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.41, B:R.47 Halogen bonds: B:I.483 OD0.49: 17 residues within 4Å: Chain B: C.126, D.127, F.128, W.179, N.234, E.235, F.246, H.311, Y.313, E.340, C.342, S.345, W.381, N.382, N.396, V.398 Ligands: CA.65 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.313 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.340, B:W.381, B:N.396 Water bridges: B:E.235

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

NA.33: 3 residues within 4Å: Chain A: P.391, N.392, F.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.392, A:N.392

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.55: 5 residues within 4Å: Chain B: T.132, V.191, N.192, W.393 Ligands: EDO.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.132, B:T.132, B:N.192

1 x CA: CALCIUM ION(Non-covalent)

CA.65: 5 residues within 4Å: Chain B: E.235, Y.244, Q.284 Ligands: EDO.42, OD0.49 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysosomal acid glucosylceramidase

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