SMTL ID : 6d7j.3 (2 other biounits)

The Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) with Glycerol in Active-Site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: D.78, A.79, D.81, V.84, Y.608 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.78, A:A.79, A:D.81, A:V.84, H2O.9 K.20: 5 residues within 4Å: Chain B: D.78, A.79, D.81, V.84, Y.608 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.78, B:A.79, B:D.81, B:V.84, H2O.27

25 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.107, D.144, P.231, E.232 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: R.523, G.561, D.562, W.563, D.603, N.604, P.605, K.766, Q.793 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: L.40, K.41, G.42, D.43, P.63 Chain B: N.85, Y.86, Y.87, E.88, R.172 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: S.525, D.527, A.528, P.555, R.556, S.558, R.559, D.560, Y.567 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: E.49, A.50, R.52, A.54, E.60, K.94 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: F.228, Y.229, N.230, P.231, L.262, G.263 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: V.25, V.109, N.139, D.141, E.205, Y.229 Ligand excluded by PLIP GOL.9: 10 residues within 4Å: Chain A: D.183, H.367, R.393, N.429, E.430, R.468, E.514, W.591, R.601, N.610 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: H.524, S.525, E.526, D.527, D.562, W.649, S.764 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain A: K.24, K.30, R.32, D.111, D.113, N.195, E.372, I.373 Ligands: GOL.16 Ligand excluded by PLIP GOL.12: 11 residues within 4Å: Chain A: L.209, E.210, S.211, F.305, G.306, R.308, H.417, N.418, H.419, P.420, R.463 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: R.304, E.345, R.349, I.373, D.376, L.377, E.380 Ligand excluded by PLIP GOL.14: 9 residues within 4Å: Chain A: Y.86, Y.87, E.88, R.172 Chain B: L.40, K.41, G.42, D.43, P.63 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: K.679, R.692, W.693, N.694 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: K.24, E.303, R.304, E.372, D.376, H.419 Ligands: GOL.11 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: T.126, V.128, D.141, I.142, T.143, D.144, A.145 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: W.433, P.434, R.469 Ligand excluded by PLIP GOL.21: 10 residues within 4Å: Chain B: D.183, H.367, R.393, N.429, E.430, R.468, E.514, W.591, R.601, N.610 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: D.441, S.443, A.444, A.447 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: V.25, V.109, N.139, D.141, L.199, E.205, Y.229 Ligand excluded by PLIP GOL.24: 12 residues within 4Å: Chain B: L.209, E.210, S.211, F.305, G.306, R.308, H.417, N.418, H.419, P.420, T.462, R.463 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain B: F.252, K.269, M.270, K.271 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: R.350, D.618, F.619, T.620 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: P.231, E.232, D.233 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: N.85 Chain B: Y.39, L.40, K.41, I.64, W.65, Q.66 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.19: 5 residues within 4Å: Chain A: D.173, M.176, P.178, S.179, D.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.173, A:D.180, A:D.180, A:D.180 NA.30: 4 residues within 4Å: Chain B: D.173, M.176, P.178, S.179 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.173, B:D.180 Water bridges: B:D.173, B:D.180

1 x PRO: PROLINE(Non-covalent)

PRO.29: 4 residues within 4Å: Chain B: E.501, M.504, Q.505, W.584 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:E.501 Hydrogen bonds: B:Q.505, P.29, P.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Little, M.S. et al., Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome. Protein Sci. (2018)

Release Date

2019-05-01

Peptides

Beta-Glucuronidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Beta-Glucuronidase

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