SMTL ID : 6szo.1

The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with D-galacturonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GTR: beta-D-galactopyranuronic acid(Non-covalent)

GTR.1: 13 residues within 4Å: Chain A: A.256, R.257, K.260, E.279, S.280, C.282, E.294, I.299, F.303, W.306, W.347, H.397 Ligands: DMS.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.260, A:E.279, A:E.294, A:W.347 Water bridges: A:H.255, A:S.280, A:C.282, A:E.294 Salt bridges: A:R.257, A:K.260, A:H.397, A:H.397

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

DMS.2: 9 residues within 4Å: Chain A: F.130, Y.131, H.255, A.256, R.257, L.258 Ligands: GTR.1, DMS.5, EDO.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.257, A:R.257, A:R.257 pi-Cation interactions: A:F.130 DMS.3: 4 residues within 4Å: Chain A: N.381, Q.402, F.406 Ligands: PGE.36 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: A.297, N.300, T.301, R.312, D.315 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.315 DMS.5: 6 residues within 4Å: Chain A: F.130, Y.131, Q.171, H.255 Ligands: DMS.2, EDO.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.131 Water bridges: A:H.255

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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.2, H2O.2, H2O.4

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

EDO.7: 4 residues within 4Å: Chain A: Y.23, T.24, L.25 Ligands: PGE.38 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: D.376, V.377, P.378, R.379 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.393, G.395, P.396, G.398, T.400 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.99, N.101, A.102, P.103, W.208 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: 6 residues within 4Å: Chain A: A.86, P.112, N.113, A.114, L.179, A.180 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: T.63, L.65, G.66, W.230, S.233, R.234, A.265, Q.268 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: P.383, S.384, G.385, R.389 Ligands: PGE.36 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: R.197, P.198, D.199 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: F.130, D.196, R.257, F.303 Ligands: PGE.37 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: A.32, L.54, P.322 Ligands: PEG.32 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain A: D.33 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: L.52, Q.53, A.56, R.62, T.63, W.264, Q.268 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: R.121, E.240, T.241, D.242, P.243, V.245 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.248, D.270, R.271, F.272, A.273, R.335 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: G.368, Q.369, T.370, G.386, A.387, W.414 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: F.73, V.75, K.90, Y.238, T.241, D.242, P.243 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: D.39, R.40, A.41 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: P.334, R.335, P.336, Q.369, W.414 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: V.115, R.118, E.120, R.121, A.122, P.123, R.249, K.416 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: Q.171, W.173, H.255, L.258, M.399 Ligands: DMS.2, DMS.5 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain A: H.45, R.46 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: H.80, T.88, N.113, I.116, A.117 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: L.201, N.202, A.206, S.207, R.217, A.221, W.222 Ligand excluded by PLIP

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

PEG.31: 7 residues within 4Å: Chain A: P.174, Q.177, A.401, Q.402, W.404, A.405, L.408 No protein-ligand interaction detected (PLIP) PEG.32: 9 residues within 4Å: Chain A: P.26, D.27, V.30, G.31, A.32, R.47, L.54, P.322 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.27, A:R.47, A:R.47 PEG.33: 4 residues within 4Å: Chain A: K.74, T.93, R.95, P.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.74, A:R.95, A:R.95 Water bridges: A:S.104 PEG.34: 6 residues within 4Å: Chain A: D.344, D.345, D.346, W.347, P.396, H.397 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.345, A:D.346, A:W.347, A:H.397

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

PGE.35: 10 residues within 4Å: Chain A: P.198, D.199, L.201, D.215, Q.216, R.217, P.304, H.305, R.309, R.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.217, A:R.217, A:R.312 PGE.36: 7 residues within 4Å: Chain A: V.380, N.381, E.382, P.383, F.406 Ligands: DMS.3, EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.383 PGE.37: 8 residues within 4Å: Chain A: F.130, Y.131, Y.189, G.191, C.194, P.195, D.196 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.189, A:D.196 PGE.38: 7 residues within 4Å: Chain A: Y.23, R.290, I.291, H.292, R.351, L.355 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.290, A:H.292, A:R.351, A:R.351

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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