SMTL ID : 7ci0.3 (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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.193, A:L.193, A:F.220, A:I.256 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.92, A:L.193, A:F.234 Hydrogen bonds: A:G.91, A:A.226 Water bridges: A:D.221, A:A.226, A:R.228 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.26, A:Y.38, A:L.41, A:V.211 Hydrogen bonds: A:V.211

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

EDO.4: 6 residues within 4Å: Chain A: R.50, E.51, L.52, A.53, V.54, I.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.52, A:I.55 Water bridges: A:A.53, A:I.55 EDO.13: 6 residues within 4Å: Chain A: A.201, S.202, A.205, F.206, R.257 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.201, A:R.257, A:R.257 Water bridges: A:A.205

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

DMS.5: 5 residues within 4Å: Chain A: R.140, S.144, P.179, A.180, D.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.140 Water bridges: A:D.181 Salt bridges: A:D.181 DMS.6: 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 DMS.8: 3 residues within 4Å: Chain A: A.49, R.50, E.51 No protein-ligand interaction detected (PLIP) DMS.15: 1 residues within 4Å: Chain A: R.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272, A:R.272

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: P.68, D.96, D.119, Y.120, R.121, L.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.120 Water bridges: A:L.97, A:D.119, A:Y.120 GOL.10: 7 residues within 4Å: Chain A: V.54, R.56, E.76, S.77, L.149, G.150, R.151 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.56, A:R.56, A:E.76, A:E.76, A:R.151, A:R.151 GOL.12: 3 residues within 4Å: Chain A: R.257, R.261 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.257, A:R.257, A:R.261, A:R.261

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

DIO.9: 3 residues within 4Å: Chain A: E.79, A.80, T.152 No protein-ligand interaction detected (PLIP) DIO.14: 3 residues within 4Å: Chain A: K.308, M.309, G.312 No protein-ligand interaction detected (PLIP)

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

PGE.11: 3 residues within 4Å: Chain A: K.265, A.266, E.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.265, A:K.265

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

SO4.16: 4 residues within 4Å: Chain A: S.145, P.146, S.147, E.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.145, A:S.147, A:S.147

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
C

Lipase

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