SMTL ID : 6tjk.1 (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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.5

5 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:R.353, A:R.353, A:R.359 Salt bridges: A:R.353 SO4.3: 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 SO4.6: 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 SO4.19: 6 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243, Y.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.188, A:K.194, A:G.243 SO4.20: 3 residues within 4Å: Chain A: H.290, K.293, V.294 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.290, A:H.290 Salt bridges: A:H.290

2 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 No protein-ligand interaction detected (PLIP) NAG.24: 1 residues within 4Å: Chain A: N.59 No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain A: L.296, F.331, P.332, N.333, T.334 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: R.39, E.41, R.47, T.482, I.483, P.485, H.490, Y.492 Ligands: EDO.17 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284 Ligands: B3P.25 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP EDO.11: 12 residues within 4Å: Chain A: A.1, R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, Y.418 Ligands: EDO.16 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: T.132, Y.133, T.134, D.137, T.183, V.191 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: L.91, N.92, A.95, N.386, P.391, I.406 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.16: 12 residues within 4Å: Chain A: C.23, D.24, S.25, F.26, L.103, K.106, S.107, S.110, E.112, G.113, K.413 Ligands: EDO.11 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: F.37, R.39, S.52, M.53, G.54, P.55, E.481, T.482 Ligands: EDO.7 Ligand excluded by PLIP EDO.18: 11 residues within 4Å: Chain A: G.80, F.81, G.115, Y.116, N.117, R.170, F.423, S.424, I.427, P.428, E.429 Ligand excluded by PLIP EDO.21: 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.22: 5 residues within 4Å: Chain A: D.358, M.361, Q.362, H.365, R.463 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: R.277, A.302, K.303, Y.304, V.305, H.306 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: L.286, L.287, H.290, W.291 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: L.314, F.316, L.317, K.346, W.348 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: K.321, G.325, Y.373, H.374 Ligand excluded by PLIP

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

B3P.25: 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.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.313 Hydrogen bonds: A:W.179, A:N.234, A:N.234, A:E.235, A:Y.244, A:Q.284, A:S.345, A:W.381 Water bridges: A:Q.247, 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
AAA

Lysosomal acid glucosylceramidase

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