SMTL ID : 6tn1.1

Unliganded Crystal Structure of Recombinant GBA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.98 Å

Oligo State

monomer

Ligands

1 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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

1 x GLN: GLUTAMINE(Covalent)

GLN.2: 5 residues within 4Å: Chain A: L.34, G.454, R.495, R.496, Q.497 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.497, A:Q.497 Hydrogen bonds: A:R.495, A:Q.497 Water bridges: A:R.496

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

NAG.3: 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

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

EDO.4: 8 residues within 4Å: Chain A: R.39, E.41, R.47, T.482, I.483, P.485, H.490, Y.492 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.39, A:E.41, A:I.483, A:I.483, A:H.490 EDO.5: 11 residues within 4Å: Chain A: R.2, C.23, D.24, S.25, L.103, K.106, S.107, S.110, E.112, G.113, K.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.24, A:K.413 Water bridges: A:S.25 EDO.8: 8 residues within 4Å: Chain A: S.196, L.240, G.250, F.251, T.252, H.255 Ligands: FMT.10, FMT.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.196, A:G.250, A:T.252, A:H.255 Water bridges: A:T.252 EDO.11: 3 residues within 4Å: Chain A: K.74, K.77, Q.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.77 Water bridges: A:K.74 EDO.20: 6 residues within 4Å: Chain A: T.132, Y.133, T.134, D.137, T.183, V.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.132, A:T.134 Water bridges: A:R.131, A:T.132, A:D.137 EDO.23: 3 residues within 4Å: Chain A: F.75, H.374, R.433 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.433, A:R.433 EDO.27: 2 residues within 4Å: Chain A: S.8, V.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.8 Water bridges: A:S.8

17 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 5 residues within 4Å: Chain A: A.302, K.303, Y.304, V.305, H.306 Ligand excluded by PLIP FMT.7: 2 residues within 4Å: Chain A: E.222, H.223 Ligand excluded by PLIP FMT.9: 2 residues within 4Å: Chain A: H.60, T.61 Ligand excluded by PLIP FMT.10: 5 residues within 4Å: Chain A: G.199, Q.200, P.201, H.255 Ligands: EDO.8 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: K.79, W.228, R.277, H.306, M.335 Ligand excluded by PLIP FMT.13: 4 residues within 4Å: Chain A: F.142, W.184, K.198, Y.205 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain A: K.194 Ligands: EDO.8 Ligand excluded by PLIP FMT.15: 7 residues within 4Å: Chain A: G.265, L.268, H.274, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: F.9, L.354, P.387, D.405, Y.412 Ligand excluded by PLIP FMT.17: 4 residues within 4Å: Chain A: H.162, L.165, Q.166, L.225 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain A: M.49, E.50, L.51 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain A: Y.11, S.12, S.13, S.356, W.357, D.358 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain A: H.290, K.293, V.294, T.297 Ligand excluded by PLIP FMT.22: 6 residues within 4Å: Chain A: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain A: I.406, T.407, K.408, D.409 Ligand excluded by PLIP FMT.25: 2 residues within 4Å: Chain A: Q.166, Q.169 Ligand excluded by PLIP FMT.26: 4 residues within 4Å: Chain A: T.36, M.53, G.54, P.55 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.28: 3 residues within 4Å: Chain A: E.235, H.311, E.340 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.340, H2O.1, H2O.1, H2O.9, H2O.14 MG.29: 6 residues within 4Å: Chain A: V.172, S.173, L.174, Q.226, F.227, W.228 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.226, H2O.7, H2O.20 MG.30: 5 residues within 4Å: Chain A: T.43, R.44, S.45, G.486, Y.487 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain A: K.194, L.240, L.241, S.242 No protein-ligand interaction detected (PLIP) MG.33: 6 residues within 4Å: Chain A: L.66, L.67, T.68, V.437, A.438, S.439 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.66, A:T.68, A:V.437, H2O.22 MG.34: 6 residues within 4Å: Chain A: L.217, Y.220, A.221, L.225, Q.226, F.227 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.217, A:L.225, H2O.12 MG.35: 7 residues within 4Å: Chain A: C.342, W.381, N.382, L.385, V.398, D.399, S.400 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.399, H2O.12

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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