SMTL ID : 6t0e.1 (1 other biounit)

The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x GCU: alpha-D-glucopyranuronic acid(Non-covalent)

GCU.1: 13 residues within 4Å: Chain A: F.130, A.256, R.257, K.260, E.279, C.282, E.294, I.299, F.303, W.306, W.347, H.397 Ligands: EDO.19 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.257, A:K.260, A:E.294, A:W.347 Water bridges: A:C.282 Salt bridges: A:R.257, A:R.257, A:H.397

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: Q.177, R.181 Ligand excluded by PLIP

1 x M55: benzyl alpha-D-glucopyranuronate(Non-covalent)

M55.3: 14 residues within 4Å: Chain A: W.148, P.150, E.152, D.196, R.197, P.198, R.257, T.301, V.302, F.303, P.304, H.305, W.306 Ligands: EDO.19 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.198 Hydrogen bonds: A:E.152, A:D.196, A:D.196, A:R.257, A:V.302, A:H.305, A:W.306 Water bridges: A:E.152

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 6 residues within 4Å: Chain A: A.180, R.181, A.405, F.406, A.409, D.412 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.181, A:R.181, A:A.409

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

EDO.5: 9 residues within 4Å: Chain A: L.201, N.202, A.206, S.207, D.210, A.212, A.213, G.214, R.217 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: P.26, V.30, G.31, A.32, R.47, L.54, P.322 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: H.80, N.113, I.116, A.117 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: A.170, Q.171, A.401 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: P.123, R.181, G.182, Y.183, R.249, D.412, L.415, K.416 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.67, P.68, E.69, G.70, M.71, F.73 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: I.116, A.119, E.120, R.121, P.243, L.244 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.219, N.310, R.313 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: R.57, E.58, D.220, N.310, R.313 Ligands: EDO.12, PEG.25 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: S.207, W.208, L.209, D.210, A.211 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: R.121, E.240, T.241, D.242, P.243 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: N.101, A.102, P.103, S.204, S.207, W.208 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: W.148, P.195, R.197, D.199, G.200, N.202, A.203 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: L.29, P.362 Ligands: PGE.28, PGE.31 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: E.152, R.257, F.303 Ligands: GCU.1, M55.3 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: K.358, E.361, P.362, R.365 Ligands: PGE.28 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: L.65, P.68, E.69, F.96, W.208, L.209 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: R.379, V.380 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain A: D.39 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.24: 9 residues within 4Å: Chain A: E.79, A.81, A.82, L.83, G.84, R.89, D.139, P.140, A.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.81, A:L.83, A:R.89, A:R.89 Water bridges: A:G.84 PEG.25: 7 residues within 4Å: Chain A: R.57, E.58, R.313, Y.314, A.320, P.322 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.320 PEG.26: 5 residues within 4Å: Chain A: G.97, R.98, D.99, A.102, W.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.98, A:D.99 Water bridges: A:G.70, A:D.99 PEG.27: 7 residues within 4Å: Chain A: Q.171, R.393, G.395, P.396, H.397, G.398, T.400 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.171 Water bridges: A:R.393, A:M.399

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.28: 6 residues within 4Å: Chain A: L.29, P.362, R.365, L.366 Ligands: EDO.18, EDO.20 No protein-ligand interaction detected (PLIP) PGE.29: 3 residues within 4Å: Chain A: K.74, V.75 Ligands: DMS.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.74 PGE.30: 11 residues within 4Å: Chain A: T.63, P.64, L.65, G.66, W.230, S.233, R.234, Q.268, D.269, R.271 Ligands: TMO.34 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.63, A:S.233, A:R.234, A:R.271 Water bridges: A:R.234 PGE.31: 8 residues within 4Å: Chain A: L.25, P.26, D.27, P.28, H.326, A.359, P.362 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.25, A:A.359

1 x MG: MAGNESIUM ION(Non-covalent)

MG.32: 4 residues within 4Å: Chain A: C.282, H.292, E.294, D.349 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.292, A:E.294, H2O.3, H2O.6, H2O.7

3 x TMO: trimethylamine oxide(Non-covalent)

TMO.33: 3 residues within 4Å: Chain A: D.33, T.35, R.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.33, A:T.35, A:R.46 Salt bridges: A:D.33 TMO.34: 8 residues within 4Å: Chain A: L.52, Q.53, A.56, R.62, T.63, W.264, Q.268 Ligands: PGE.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.63 Water bridges: A:R.62 TMO.35: 6 residues within 4Å: Chain A: P.334, R.335, P.336, Q.369, A.387, W.414 No protein-ligand interaction detected (PLIP)

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.36: 3 residues within 4Å: Chain A: V.75, M.78 Ligands: PGE.29 No protein-ligand interaction detected (PLIP) DMS.37: 1 residues within 4Å: Chain A: R.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.365, A:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazurkewich, S. et al., Structural and biochemical studies of the glucuronoyl esteraseOtCE15A illuminate its interaction with lignocellulosic components. J.Biol.Chem. (2019)

Release Date

2019-11-27

Peptides

glucuronoyl esterase OtCE15A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

glucuronoyl esterase OtCE15A

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