SMTL ID : 6keu.1

Wildtype E53, a microbial HSL esterase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x D8F: (4-nitrophenyl) hexanoate(Non-covalent)

D8F.1: 11 residues within 4Å: Chain A: Y.35, G.87, G.88, S.159, A.160, L.190, V.208, L.209, F.217, H.281, S.282 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.35, A:A.160, A:L.209, A:L.209, A:F.217, A:F.217 Salt bridges: A:H.281 D8F.6: 10 residues within 4Å: Chain B: Y.35, G.87, G.88, S.159, A.160, L.190, L.209, F.217, H.281, S.282 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.35, B:A.160, B:L.209, B:F.217, B:F.217 Water bridges: B:Y.35 Salt bridges: B:H.281 D8F.15: 13 residues within 4Å: Chain C: Y.35, G.87, G.88, I.91, S.159, A.160, L.190, V.208, L.209, I.214, F.217, H.281, S.282 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.35, C:I.91, C:A.160, C:L.209, C:F.217, C:F.217 Water bridges: C:Y.35 Salt bridges: C:H.281 D8F.21: 12 residues within 4Å: Chain D: Y.35, G.87, G.88, I.91, S.159, A.160, L.190, V.208, L.209, F.217, H.281, S.282 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.35, D:I.91, D:A.160, D:L.209, D:F.217, D:F.217 Salt bridges: D:H.281

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

SO4.2: 4 residues within 4Å: Chain A: A.71, R.72, E.73, S.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.72, A:E.73, A:S.74 SO4.7: 2 residues within 4Å: Chain B: R.47, E.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.48, B:E.48 Salt bridges: B:R.47 SO4.8: 2 residues within 4Å: Chain A: E.277 Chain B: R.269 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.269, B:R.269 Salt bridges: B:R.269 SO4.9: 1 residues within 4Å: Chain B: R.72 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.72 SO4.22: 3 residues within 4Å: Chain D: T.27, L.28 Ligands: EDO.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.28 Water bridges: D:E.29 SO4.23: 1 residues within 4Å: Chain D: R.72 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.72

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

EDO.3: 3 residues within 4Å: Chain A: R.137, P.176, A.177 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: R.254, R.258 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: A.50, R.72, E.73, S.74 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: R.5, S.292, G.295, D.296 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: T.27, E.29, E.30 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: I.4, K.9, L.12, E.13, G.206, F.207 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: G.20, T.22 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: R.137, P.176, A.177 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain C: E.76, A.77, T.149 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: R.47, A.106, L.107 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain C: R.299 Chain D: M.306, M.307 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain D: R.137, P.176, A.177 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain D: A.50, R.72, E.73, S.74 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain D: R.254, R.258 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain D: P.143, S.144, E.145 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain D: A.46, D.95, H.98, N.99 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain D: I.52, N.54, R.67, H.98 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: L.23, M.26, T.27, L.28, F.216 Ligands: SO4.22 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.93, D.116, Y.117, R.118, L.119 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.93, A:D.93, A:L.94, A:D.116

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

6NA.20: 5 residues within 4Å: Chain C: A.198, A.202, F.203, R.254, R.258 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.198, C:A.202, C:F.203 Water bridges: C:R.258 Salt bridges: C:R.254, C:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X.C. et al., Wildtype E53, a microbial HSL esterase. To Be Published

Release Date

2020-07-08

Peptides

Lipase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Lipase