SMTL ID : 6d7j.1 (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-tetramer

Ligands

4 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.16: 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.30 K.34: 5 residues within 4Å: Chain C: D.78, A.79, D.81, V.84, Y.608 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.78, C:A.79, C:D.81, C:V.84, H2O.50 K.53: 5 residues within 4Å: Chain D: D.78, A.79, D.81, V.84, Y.608 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.78, D:A.79, D:D.81, D:V.84, H2O.68

53 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: N.85, Y.86, Y.87, E.88, R.172 Chain B: L.40, K.41, G.42, D.43, P.63 Ligands: GOL.13 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: V.123, Y.124, T.125, T.126, A.148, F.149, S.152, D.154 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: F.228, Y.229, N.230, P.231, L.262, G.263 Chain D: A.447 Ligands: GOL.55 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: I.99, N.101, G.106, R.107, I.108, T.143, V.146, K.147 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: V.128, D.141, I.142, T.143, D.144, A.145 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: D.183, H.367, R.393, N.429, E.430, R.468, E.514, W.591 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: D.264, Q.265 Chain D: K.450, H.453, D.454, H.457 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: R.523, G.561, D.562, W.563, P.605, K.766, Q.793 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: D.441, S.443, A.444 Chain D: P.231 Ligands: GOL.60 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: E.232, D.233, I.234, R.235 Ligands: GOL.12 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: P.231, E.232, D.233 Chain D: S.443 Ligands: GOL.11, GOL.55 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: K.41, D.78, V.84, N.85, Y.87 Chain B: K.41 Ligands: GOL.2 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: S.483, I.484, W.485, Y.489, R.490 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: I.31, L.33, L.96, L.97, A.98, L.196 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: R.107, D.141, D.144, Y.229, P.231 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain B: E.205, F.228, Y.229, N.230, P.231, P.261, L.262, G.263 Chain C: A.447 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: K.30, R.32, D.111, D.113, Y.193, N.195, I.373 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: D.183, H.367, R.393, N.429, E.430, R.468, E.514, W.591 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: R.523, G.561, D.562, W.563, D.603, P.605, K.766, Q.793 Ligand excluded by PLIP GOL.24: 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.25: 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 GOL.26: 11 residues within 4Å: Chain B: L.209, E.210, S.211, F.305, G.306, H.417, N.418, H.419, P.420, T.462, R.463 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain B: T.310, E.311, F.312, D.461, T.462, R.463, M.464 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain B: D.432, W.433, P.434, R.469 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain B: E.724, Q.726, A.728, G.759, I.760, R.761 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: C.736, Q.737, V.738, A.822 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain B: K.767, Q.768, E.817 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain B: A.23, V.25, P.26, N.139, L.199, F.204, E.205, Y.229 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain C: R.107, D.144, P.231, E.232 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain C: R.523, G.561, D.562, W.563, D.603, N.604, P.605, K.766, Q.793 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain C: L.40, K.41, G.42, D.43, P.63 Chain D: N.85, Y.86, Y.87, E.88, R.172 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain C: S.525, D.527, A.528, P.555, R.556, S.558, R.559, D.560, Y.567 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain C: E.49, A.50, R.52, A.54, E.60, K.94 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain B: A.447 Chain C: F.228, Y.229, N.230, P.231, L.262, G.263 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain C: V.25, V.109, N.139, D.141, E.205, Y.229 Ligand excluded by PLIP GOL.42: 10 residues within 4Å: Chain C: 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.43: 7 residues within 4Å: Chain C: H.524, S.525, E.526, D.527, D.562, W.649, S.764 Ligand excluded by PLIP GOL.44: 9 residues within 4Å: Chain C: K.24, K.30, R.32, D.111, D.113, N.195, E.372, I.373 Ligands: GOL.49 Ligand excluded by PLIP GOL.45: 11 residues within 4Å: Chain C: 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.46: 7 residues within 4Å: Chain C: R.304, E.345, R.349, I.373, D.376, L.377, E.380 Ligand excluded by PLIP GOL.47: 9 residues within 4Å: Chain C: Y.86, Y.87, E.88, R.172 Chain D: L.40, K.41, G.42, D.43, P.63 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain C: K.679, R.692, W.693, N.694 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain C: K.24, E.303, R.304, E.372, D.376, H.419 Ligands: GOL.44 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain C: T.126, V.128, D.141, I.142, T.143, D.144, A.145 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain C: W.433, P.434, R.469 Ligand excluded by PLIP GOL.54: 10 residues within 4Å: Chain D: 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.55: 8 residues within 4Å: Chain A: N.230, P.231 Chain D: D.441, S.443, A.444, A.447 Ligands: GOL.4, GOL.12 Ligand excluded by PLIP GOL.56: 7 residues within 4Å: Chain D: V.25, V.109, N.139, D.141, L.199, E.205, Y.229 Ligand excluded by PLIP GOL.57: 12 residues within 4Å: Chain D: 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.58: 4 residues within 4Å: Chain D: F.252, K.269, M.270, K.271 Ligand excluded by PLIP GOL.59: 4 residues within 4Å: Chain D: R.350, D.618, F.619, T.620 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain A: S.443 Chain D: P.231, E.232, D.233 Ligands: GOL.10 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain C: N.85 Chain D: Y.39, L.40, K.41, I.64, W.65, Q.66 Ligand excluded by PLIP

2 x PRO: PROLINE(Non-covalent)

PRO.14: 12 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, T.462, R.463 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:P.420 Hydrogen bonds: A:L.209, A:S.211, A:T.462 Water bridges: A:R.308 Salt bridges: A:H.417, A:R.463 PRO.62: 4 residues within 4Å: Chain D: E.501, M.504, Q.505, W.584 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:E.501 Hydrogen bonds: D:Q.505, P.62, P.62

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

NA.15: 4 residues within 4Å: Chain A: D.173, M.176, P.178, S.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.173, A:P.178 Water bridges: A:D.180 NA.33: 4 residues within 4Å: Chain B: D.173, M.176, P.178, S.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.180, B:D.180 Water bridges: B:D.173 NA.52: 5 residues within 4Å: Chain C: D.173, M.176, P.178, S.179, D.180 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.173, C:D.180, C:D.180, C:D.180 NA.63: 4 residues within 4Å: Chain D: D.173, M.176, P.178, S.179 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.173, D:D.180 Water bridges: D:D.173, D:D.180

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-Glucuronidase

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