SMTL ID : 3rga.1

Crystal structure of epoxide hydrolase for polyether lasalocid A biosynthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x LSB: (4R,5S)-3-[(2R,3S,4S)-2-ethyl-5-[(3R)-2-ethyl-3-[2-[(2R,3R)-2-ethyl-3-methyl-oxiran-2-yl]ethyl]oxiran-2-yl]-3-hydroxy-4-methyl-pentanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one(Non-covalent)

LSB.1: 17 residues within 4Å: Chain A: Y.15, C.16, D.39, L.56, A.59, E.66, L.82, A.84, V.86, V.88, T.101, V.103, G.105, I.107, M.118, V.120, W.122 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.56, A:A.59, A:L.82, A:A.84, A:T.101, A:V.103, A:V.103, A:I.107, A:V.120, A:W.122 Hydrogen bonds: A:Y.15, A:D.39

1 x ILD: (4R,5S)-3-[(2R)-2-{(2S,2'R,4S,5S,5'R)-2,5'-diethyl-5'-[(1S)-1-hydroxyethyl]-4-methyloctahydro-2,2'-bifuran-5-yl}butanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one(Non-covalent)

ILD.2: 20 residues within 4Å: Chain A: H.75, D.171, P.172, S.175, W.176, R.178, H.187, M.190, A.191, E.198, M.220, S.225, L.229, H.232, L.234, I.250, Y.252, W.271 Ligands: ACT.6, FMT.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.176, A:A.191, A:L.229, A:H.232, A:L.234, A:Y.252, A:Y.252 Hydrogen bonds: A:D.171, A:R.178 pi-Stacking: A:W.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.168, F.169, E.170, T.177, E.266, M.267, R.268 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.168, A:R.168, A:R.168, A:E.170, A:T.177 GOL.4: 4 residues within 4Å: Chain A: R.132, E.137, G.206, Q.207 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.132, A:R.132, A:E.137, A:G.206 Water bridges: A:R.132, A:Q.207, A:Q.207

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: R.36, V.38, P.45, E.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.117 Salt bridges: A:R.36 ACT.6: 4 residues within 4Å: Chain A: H.75, H.232, H.233 Ligands: ILD.2 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.75, A:H.232, A:H.233

2 x MOH: METHANOL(Non-functional Binders)

MOH.7: 5 residues within 4Å: Chain A: E.138, K.141, R.145, T.203 Ligands: FMT.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.145, A:T.203, A:T.203 MOH.8: 3 residues within 4Å: Chain A: D.136, R.139, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.140, A:R.140

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.9: 4 residues within 4Å: Chain A: E.138, K.141, T.203 Ligands: MOH.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.203 Water bridges: A:K.141 FMT.10: 6 residues within 4Å: Chain A: H.147, I.151, H.187, A.191, E.198 Ligands: ILD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.187 FMT.11: 2 residues within 4Å: Chain A: R.178, H.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:H.187

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

NA.12: 4 residues within 4Å: Chain A: V.124, T.125, S.127, T.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.124, A:S.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hotta, K. et al., Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis. Nature (2012)

Release Date

2012-03-07

Peptides

Epoxide hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epoxide hydrolase