SMTL ID : 6tjk.2 (1 other biounit)

Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 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: 7 residues within 4Å: Chain A: R.2, I.5, N.19, A.20, T.21, Y.22 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22

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

EDO.2: 5 residues within 4Å: Chain A: L.314, F.316, L.317, K.346, W.348 Ligand excluded by PLIP EDO.6: 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.7: 9 residues within 4Å: Chain A: L.268, A.269, H.273, H.274, N.275, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: H.162, L.165, Q.166, K.224, L.225 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: L.165, A.168, R.170, P.171, V.172 Ligand excluded by PLIP EDO.10: 12 residues within 4Å: Chain A: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, F.417, Y.418 Ligands: EDO.16 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: F.75, L.372, Y.373, H.374, R.433 Ligands: EDO.19 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: K.7, F.9, L.354, P.387, D.405, Y.412 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: I.130, R.131, T.132, W.393 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.44, S.45, G.486, Y.487 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: P.3, C.4, D.24, G.46, R.47, R.48, E.50 Ligands: EDO.10 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: L.91, N.92, A.95, N.386, G.390, P.391, I.406 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: I.5, P.6, K.7, V.17 Ligands: NAG-NAG-BMA-MAN.1 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: F.75, H.328, H.374 Ligands: EDO.11 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: R.170, P.171, P.428, E.429, P.452 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284 Ligands: B3P.28 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain A: R.39, E.41, R.47, T.482, I.483, P.485, H.490, Y.492 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: F.37, R.39, S.52, M.53, G.54, P.55, E.481 Ligands: EDO.23 Ligand excluded by PLIP EDO.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: L.296, A.302, F.331, P.332, N.333, T.334 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain A: S.196, G.199, Q.200, P.201, H.206, H.255 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: S.196, L.240, G.250, F.251, T.252, H.255 Ligands: EDO.31 Ligand excluded by PLIP

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

SO4.3: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.356, A:W.357, A:D.358 Water bridges: A:S.12, A:R.353, A:R.353, A:R.359 Salt bridges: A:R.353 SO4.5: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:K.79, A:K.79 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.25: 5 residues within 4Å: Chain A: D.358, M.361, Q.362, H.365, R.463 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.358 Salt bridges: A:R.463 SO4.26: 4 residues within 4Å: Chain A: L.286, L.287, H.290, W.291 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.290, A:W.291 Salt bridges: A:H.290 SO4.27: 6 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243, Y.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.194, A:S.242, A:G.243 Water bridges: A:N.192

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

NAG.4: 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

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.28: 19 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, Y.244, F.246, Q.247, Q.284, H.311, Y.313, E.340, C.342, S.345, K.346, W.381, N.396, V.398 Ligands: EDO.21 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.313 Hydrogen bonds: A:W.179, A:N.234, A:N.234, A:Y.244, A:Y.244, A:Y.244, A:S.345, A:S.345, A:W.381 Water bridges: A:E.235, A:E.235, A:N.396

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

Lysosomal acid glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Lysosomal acid glucosylceramidase

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