SMTL ID : 3gxd.1

Crystal structure of Apo acid-beta-glucosidase pH 4.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

50 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.2: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: T.63, G.64, L.65, Q.440 Ligand excluded by PLIP PO4.4: 5 residues within 4Å: Chain A: K.79, W.228, R.277, H.306, E.429 Ligand excluded by PLIP PO4.5: 1 residues within 4Å: Chain A: K.473 Ligand excluded by PLIP PO4.6: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.7: 5 residues within 4Å: Chain A: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.8: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP PO4.9: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP PO4.11: 2 residues within 4Å: Chain A: S.45, R.47 Ligand excluded by PLIP PO4.12: 1 residues within 4Å: Chain A: E.72 Ligand excluded by PLIP PO4.13: 2 residues within 4Å: Chain A: R.170, P.428 Ligand excluded by PLIP PO4.14: 6 residues within 4Å: Chain A: R.395, N.396 Chain D: N.392, W.393, V.394, R.395 Ligand excluded by PLIP PO4.15: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.18: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.19: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.21: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.22: 2 residues within 4Å: Chain B: K.321, R.329 Ligand excluded by PLIP PO4.23: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.24: 4 residues within 4Å: Chain B: R.277, K.303, V.305, H.306 Ligand excluded by PLIP PO4.25: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP PO4.26: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain B: A.1, R.2, C.23, S.25 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.31: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.32: 2 residues within 4Å: Chain C: R.44, S.45 Ligand excluded by PLIP PO4.33: 2 residues within 4Å: Chain C: E.254, R.257 Ligand excluded by PLIP PO4.34: 6 residues within 4Å: Chain C: Q.226, F.227, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.35: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.36: 3 residues within 4Å: Chain C: R.277, V.305, H.306 Ligand excluded by PLIP PO4.37: 2 residues within 4Å: Chain C: H.290, K.293 Ligand excluded by PLIP PO4.38: 3 residues within 4Å: Chain C: A.438, N.442, L.444 Ligand excluded by PLIP PO4.39: 3 residues within 4Å: Chain C: I.158, P.159, H.162 Ligand excluded by PLIP PO4.40: 3 residues within 4Å: Chain C: F.75, H.328, H.374 Ligand excluded by PLIP PO4.41: 3 residues within 4Å: Chain C: Q.169, R.170, P.428 Ligand excluded by PLIP PO4.43: 5 residues within 4Å: Chain C: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.44: 7 residues within 4Å: Chain C: S.242 Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.45: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP PO4.46: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.48: 5 residues within 4Å: Chain D: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.49: 3 residues within 4Å: Chain D: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.50: 3 residues within 4Å: Chain D: R.277, V.305, H.306 Ligand excluded by PLIP PO4.51: 3 residues within 4Å: Chain D: I.158, P.159, H.162 Ligand excluded by PLIP PO4.52: 1 residues within 4Å: Chain D: R.262 Ligand excluded by PLIP PO4.53: 2 residues within 4Å: Chain D: K.321, R.329 Ligand excluded by PLIP PO4.54: 3 residues within 4Å: Chain D: T.187, K.198, G.199 Ligand excluded by PLIP

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

NAG.16: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:T.21 NAG.28: 4 residues within 4Å: Chain B: N.146 Chain C: L.94, L.96, P.98 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain B: I.5, N.19, Y.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.19 NAG.42: 4 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.21 NAG.55: 7 residues within 4Å: Chain A: A.95, L.96, S.97, P.98 Chain D: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP) NAG.56: 4 residues within 4Å: Chain D: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.19, D:N.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry (2009)

Release Date

2009-05-05

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucosylceramidase

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