SMTL ID : 2nt1.5 (4 other biounits)

Structure of acid-beta-glucosidase at neutral pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.19, T.21, Y.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:N.19, A:T.21 NAG.23: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.19, B:T.21 NAG.42: 3 residues within 4Å: Chain C: N.19, T.21, Y.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.19 Water bridges: C:N.19, C:T.21 NAG.66: 4 residues within 4Å: Chain D: I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.19

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

PO4.2: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.3: 3 residues within 4Å: Chain A: T.63, G.64, Q.440 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.5: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP PO4.6: 2 residues within 4Å: Chain A: R.44, 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: 3 residues within 4Å: Chain A: F.75, H.328, H.374 Ligand excluded by PLIP PO4.9: 3 residues within 4Å: Chain A: L.165, P.171, V.172 Ligand excluded by PLIP PO4.10: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP PO4.11: 2 residues within 4Å: Chain A: A.438, N.442 Ligand excluded by PLIP PO4.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.13: 2 residues within 4Å: Chain A: Q.57, A.58 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP PO4.15: 3 residues within 4Å: Chain A: E.254, R.257 Chain B: K.441 Ligand excluded by PLIP PO4.16: 2 residues within 4Å: Chain A: R.329, L.330 Ligand excluded by PLIP PO4.17: 6 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 Chain D: T.407, K.408 Ligand excluded by PLIP PO4.18: 10 residues within 4Å: Chain A: D.87, P.122, A.124, S.125, Y.133, Y.135, P.150, E.152, D.153, K.157 Ligand excluded by PLIP PO4.19: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP PO4.20: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.21: 8 residues within 4Å: Chain A: A.84, R.120, S.339, E.340, A.341, T.379, D.380, W.381 Ligand excluded by PLIP PO4.22: 2 residues within 4Å: Chain A: R.170, P.428 Ligand excluded by PLIP PO4.24: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.25: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.26: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.27: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP PO4.28: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.29: 4 residues within 4Å: Chain B: T.187, K.194, G.195, S.196 Ligand excluded by PLIP PO4.30: 3 residues within 4Å: Chain B: T.187, K.198, G.199 Ligand excluded by PLIP PO4.31: 2 residues within 4Å: Chain B: H.290, K.293 Ligand excluded by PLIP PO4.32: 4 residues within 4Å: Chain B: F.331, P.332, N.333, T.334 Ligand excluded by PLIP PO4.33: 3 residues within 4Å: Chain B: R.277, V.305, H.306 Ligand excluded by PLIP PO4.34: 1 residues within 4Å: Chain B: R.262 Ligand excluded by PLIP PO4.35: 3 residues within 4Å: Chain B: P.98, P.99, N.102 Ligand excluded by PLIP PO4.36: 4 residues within 4Å: Chain B: L.165, R.170, P.171, V.172 Ligand excluded by PLIP PO4.37: 2 residues within 4Å: Chain B: Q.207, R.211 Ligand excluded by PLIP PO4.38: 2 residues within 4Å: Chain B: K.321, R.329 Ligand excluded by PLIP PO4.39: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.40: 3 residues within 4Å: Chain B: A.438, N.442, L.444 Ligand excluded by PLIP PO4.41: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP PO4.43: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.44: 3 residues within 4Å: Chain C: T.63, G.64, Q.440 Ligand excluded by PLIP PO4.45: 2 residues within 4Å: Chain C: R.44, S.45 Ligand excluded by PLIP PO4.46: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain C: Q.226, T.272, H.273, V.276 Ligand excluded by PLIP PO4.48: 5 residues within 4Å: Chain C: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.49: 2 residues within 4Å: Chain C: R.170, P.428 Ligand excluded by PLIP PO4.50: 2 residues within 4Å: Chain C: Q.57, A.58 Ligand excluded by PLIP PO4.51: 3 residues within 4Å: Chain C: S.465, K.466, D.467 Ligand excluded by PLIP PO4.52: 3 residues within 4Å: Chain C: I.158, P.159, H.162 Ligand excluded by PLIP PO4.53: 2 residues within 4Å: Chain C: A.438, N.442 Ligand excluded by PLIP PO4.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.55: 3 residues within 4Å: Chain C: T.252, E.254, H.255 Ligand excluded by PLIP PO4.56: 2 residues within 4Å: Chain C: E.254, R.257 Ligand excluded by PLIP PO4.57: 3 residues within 4Å: Chain C: R.277, V.305, H.306 Ligand excluded by PLIP PO4.58: 6 residues within 4Å: Chain B: T.407, K.408 Chain C: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.59: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.60: 3 residues within 4Å: Chain C: F.75, H.328, H.374 Ligand excluded by PLIP PO4.61: 8 residues within 4Å: Chain C: G.83, A.84, R.120, S.339, E.340, T.379, D.380, W.381 Ligand excluded by PLIP PO4.62: 10 residues within 4Å: Chain C: D.87, P.122, A.124, S.125, Y.133, Y.135, P.150, E.152, D.153, K.157 Ligand excluded by PLIP PO4.63: 4 residues within 4Å: Chain C: L.165, R.170, P.171, V.172 Ligand excluded by PLIP PO4.64: 8 residues within 4Å: Chain B: E.151 Chain C: D.87, L.91, S.129, I.130, R.131, Y.133, E.152 Ligand excluded by PLIP PO4.65: 2 residues within 4Å: Chain C: H.290, K.293 Ligand excluded by PLIP PO4.67: 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 PO4.68: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.69: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.70: 5 residues within 4Å: Chain D: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.71: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP PO4.72: 3 residues within 4Å: Chain D: I.158, P.159, H.162 Ligand excluded by PLIP PO4.73: 3 residues within 4Å: Chain D: P.289, H.290, K.293 Ligand excluded by PLIP PO4.74: 3 residues within 4Å: Chain D: T.187, K.198, G.199 Ligand excluded by PLIP PO4.75: 5 residues within 4Å: Chain D: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.76: 2 residues within 4Å: Chain D: Q.207, R.211 Ligand excluded by PLIP PO4.77: 3 residues within 4Å: Chain D: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.78: 3 residues within 4Å: Chain D: L.165, P.171, V.172 Ligand excluded by PLIP PO4.79: 3 residues within 4Å: Chain D: R.277, V.305, H.306 Ligand excluded by PLIP PO4.80: 4 residues within 4Å: Chain D: T.187, K.194, G.195, S.196 Ligand excluded by PLIP PO4.81: 3 residues within 4Å: Chain D: A.438, N.442, L.444 Ligand excluded by PLIP PO4.82: 9 residues within 4Å: Chain D: P.3, C.4, I.5, C.16, V.17, C.18, Y.22, C.23, D.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Nat.Chem.Biol. (2007)

Release Date

2006-12-26

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucosylceramidase

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