SMTL ID : 6syv.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: C.282, H.292, E.294, T.295, D.349 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.292, A:E.294, H2O.1, H2O.10, H2O.13

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

EDO.2: 5 residues within 4Å: Chain A: A.102, P.103, S.104, Q.106, R.147 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.104, A:R.147, A:R.147 Water bridges: A:N.101, A:A.102, A:S.104, A:S.104 EDO.3: 2 residues within 4Å: Chain A: D.99, P.100 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: A.32, L.54, P.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.32 EDO.5: 5 residues within 4Å: Chain A: L.65, P.68, E.69, W.208, L.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.69 Water bridges: A:F.96 EDO.6: 3 residues within 4Å: Chain A: L.25, P.26, D.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.25, A:D.27 Water bridges: A:H.326 EDO.7: 3 residues within 4Å: Chain A: H.45, R.46 Ligands: PEG.16 No protein-ligand interaction detected (PLIP) EDO.8: 10 residues within 4Å: Chain A: P.123, R.181, G.182, Y.183, R.249, A.411, D.412, L.415, K.416, S.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181, A:D.412, A:L.415 EDO.9: 5 residues within 4Å: Chain A: D.345, W.347, H.397 Ligands: GCU.13, BDP.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.397 EDO.10: 3 residues within 4Å: Chain A: N.381, Q.402, F.406 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.402, A:Q.402 EDO.11: 6 residues within 4Å: Chain A: P.334, R.335, P.336, Q.369, A.387, W.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.369 EDO.12: 2 residues within 4Å: Chain A: D.215, Q.216 No protein-ligand interaction detected (PLIP)

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

GCU.13: 14 residues within 4Å: Chain A: F.130, A.256, R.257, K.260, S.280, C.282, E.294, I.299, F.303, W.306, W.347, H.397 Ligands: EDO.9, BDP.14 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.257, A:K.260, A:S.280, A:E.294, A:W.347 Water bridges: A:C.282, A:E.294, A:E.294, A:E.294, A:E.294, A:H.397, A:H.397 Salt bridges: A:R.257, A:R.257, A:H.397

1 x BDP: beta-D-glucopyranuronic acid(Non-covalent)

BDP.14: 12 residues within 4Å: Chain A: F.130, A.256, R.257, K.260, E.294, I.299, F.303, W.306, W.347, H.397 Ligands: EDO.9, GCU.13 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.257, A:K.260, A:S.280, A:E.294, A:W.347 Water bridges: A:C.282, A:E.294, A:E.294, A:E.294, A:H.397, A:H.397 Salt bridges: A:R.257, A:R.257, A:H.397

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

PEG.15: 7 residues within 4Å: Chain A: L.201, N.202, A.206, S.207, G.214, D.215, R.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.201, A:N.202 PEG.16: 5 residues within 4Å: Chain A: A.41, T.42, H.45, R.46 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.41 PEG.17: 4 residues within 4Å: Chain A: S.21, Y.23, T.24, L.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.21, A:L.25 Water bridges: A:Y.23

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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