SMTL ID : 6t0e.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

GCU.1: 12 residues within 4Å: Chain A: F.130, A.256, R.257, K.260, C.282, E.294, I.299, F.303, W.306, W.347, H.397 Ligands: PGE.19 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.257, A:K.260, A:E.294 Water bridges: A:C.282 Salt bridges: A:R.257, A:R.257, A:H.397

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

EDO.2: 3 residues within 4Å: Chain A: E.413, W.414, K.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.413 EDO.3: 9 residues within 4Å: Chain A: L.201, N.202, S.204, A.206, S.207, D.210, A.212, G.214, R.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.210, A:G.214 Water bridges: A:D.210 EDO.4: 7 residues within 4Å: Chain A: Y.338, P.383, R.389, F.406, A.409, F.410 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.338, A:R.389, A:A.409, A:F.410 Water bridges: A:A.409 EDO.5: 5 residues within 4Å: Chain A: A.151, A.153, P.154, N.155, G.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.151, A:N.155, A:N.155 EDO.6: 7 residues within 4Å: Chain A: R.57, E.58, R.313, Y.314, P.322 Ligands: EDO.10, EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.57, A:E.58 EDO.7: 10 residues within 4Å: Chain A: R.121, L.239, E.240, T.241, D.242, P.243, V.245, D.246, A.247, S.248 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.121, A:E.240, A:D.242, A:D.246, A:A.247 EDO.8: 7 residues within 4Å: Chain A: R.48, L.52, A.267, Q.268, D.269, D.270 Ligands: DMS.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.48, A:R.48, A:Q.268, A:D.270 EDO.9: 5 residues within 4Å: Chain A: P.383, S.384, G.385, R.389 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.384, A:G.385 EDO.10: 5 residues within 4Å: Chain A: R.313, Y.314, H.317, A.320 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313, A:H.317 EDO.11: 7 residues within 4Å: Chain A: P.26, V.30, G.31, A.32, R.47, L.54, P.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.47, A:R.47 EDO.12: 6 residues within 4Å: Chain A: E.343, V.377, P.378, R.379, V.380, I.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.343 EDO.13: 3 residues within 4Å: Chain A: T.24, L.25, A.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.24, A:T.24 EDO.14: 6 residues within 4Å: Chain A: V.75, K.90, Y.238, T.241, D.242, P.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.90 EDO.15: 5 residues within 4Å: Chain A: R.57, E.58, N.310, R.313 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.313, A:R.313 Water bridges: A:N.310, A:N.310 EDO.16: 4 residues within 4Å: Chain A: P.174, V.175, E.176, Q.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.174, A:E.176, A:Q.177

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

PEG.17: 6 residues within 4Å: Chain A: Q.171, K.172, G.398, M.399, T.400, A.401 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.399, A:A.401 Water bridges: A:R.393 PEG.18: 13 residues within 4Å: Chain A: V.115, R.118, A.122, P.123, R.181, G.182, Y.183, R.249, A.411, D.412, L.415, K.416, S.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.182, A:D.412 Water bridges: A:R.118, A:R.249

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

PGE.19: 12 residues within 4Å: Chain A: F.130, Y.131, P.154, S.168, D.169, Q.171, K.172, H.255, A.256, H.397, G.398 Ligands: GCU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.131, A:D.169, A:K.172, A:H.255

4 x TMO: trimethylamine oxide(Non-covalent)

TMO.20: 5 residues within 4Å: Chain A: A.146, R.147, W.148, H.159, R.160 No protein-ligand interaction detected (PLIP) TMO.21: 4 residues within 4Å: Chain A: H.38, D.39, R.40, L.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 TMO.22: 5 residues within 4Å: Chain A: S.207, W.208, L.209, D.210, A.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.208 Water bridges: A:A.211 TMO.23: 8 residues within 4Å: Chain A: L.52, Q.53, A.56, G.61, R.62, T.63, W.264, Q.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.63, A:Q.268

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

DMS.24: 7 residues within 4Å: Chain A: S.233, R.234, Q.268, D.269, D.270, R.271 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.234, A:R.271 Water bridges: A:R.234 Salt bridges: A:D.269 DMS.25: 4 residues within 4Å: Chain A: V.75, T.76, T.77, M.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.78 DMS.26: 5 residues within 4Å: Chain A: L.65, P.68, E.69, W.208, L.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.69

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
B

glucuronoyl esterase OtCE15A

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