SMTL ID : 7ci0.1 (3 other biounits)

Microbial Hormone-sensitive lipase E53 mutant S162A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x NPO: P-NITROPHENOL(Non-covalent)

NPO.1: 14 residues within 4Å: Chain A: G.91, A.162, A.163, L.193, A.197, L.212, I.217, F.220, D.221, R.228, F.234, I.256, H.284 Ligands: NPO.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.193, A:F.220, A:F.220, A:I.256 Water bridges: A:R.228 NPO.2: 13 residues within 4Å: Chain A: G.91, F.92, A.163, N.166, L.193, F.220, D.221, Y.224, A.226, R.228, G.233, F.234 Ligands: NPO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.92, A:L.193, A:Y.224, A:F.234 Hydrogen bonds: A:G.91 Water bridges: A:D.221, A:A.226 pi-Stacking: A:Y.224 NPO.3: 11 residues within 4Å: Chain A: L.26, Y.38, L.41, G.90, I.94, V.211, L.212, S.216, F.220, H.284, S.285 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.41, A:V.211 Water bridges: A:S.37

2 x 6NA: HEXANOIC ACID(Non-covalent)

6NA.4: 6 residues within 4Å: Chain A: A.201, S.202, A.205, F.206, R.257, R.261 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.201, A:A.205 Water bridges: A:R.257 Salt bridges: A:R.257, A:R.261 6NA.12: 8 residues within 4Å: Chain A: G.95, D.96, L.97, D.119, Y.120, R.121, L.122, H.126 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.96, A:L.122 Hydrogen bonds: A:L.122 Salt bridges: A:H.126

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

PEG.5: 3 residues within 4Å: Chain A: R.228, A.229, L.237 No protein-ligand interaction detected (PLIP)

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

EDO.6: 2 residues within 4Å: Chain A: L.277, R.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.302, A:R.302 EDO.10: 4 residues within 4Å: Chain A: G.62, P.63, A.64, G.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.62 Water bridges: A:G.65

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

DMS.7: 5 residues within 4Å: Chain A: R.140, S.144, P.179, A.180, D.181 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.181 DMS.8: 5 residues within 4Å: Chain A: A.53, A.74, R.75, E.76, S.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.75

3 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.9: 3 residues within 4Å: Chain A: E.79, A.80, T.152 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.152 DIO.11: 1 residues within 4Å: Chain A: E.269 No protein-ligand interaction detected (PLIP) DIO.13: 2 residues within 4Å: Chain A: R.50, E.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.51

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain A: P.63, E.133 No protein-ligand interaction detected (PLIP) GOL.15: 8 residues within 4Å: Chain A: V.54, R.56, L.71, E.76, S.77, L.149, G.150, R.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.56, A:R.56, A:R.151, A:R.151 GOL.16: 4 residues within 4Å: Chain A: M.29, T.30, L.31, E.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.31 Water bridges: A:A.27, A:M.29, A:T.30, A:E.32 GOL.17: 1 residues within 4Å: Chain A: K.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.265

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 1 residues within 4Å: Chain A: R.272 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.272, A:R.272, A:R.272 Salt bridges: A:R.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, Y. et al., Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus . Front Microbiol (2021)

Release Date

2021-07-14

Peptides

Lipase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lipase

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