SMTL ID : 7w8n.1

Microbial Hormone-sensitive lipase E53 wild type

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-1-mer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: D.96, D.119, Y.120, R.121, L.122 7 PLIP interactions: 7 interactions with chain A Water bridges: A:D.96, A:D.96, A:L.97, A:D.119, A:D.119, A:D.119, A:D.119 GOL.39: 9 residues within 4Å: Chain B: L.193, D.196, A.197, V.198, I.217, E.218, D.221, R.228, F.234 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.197, B:D.221, B:R.228, B:R.228 Water bridges: B:D.221 GOL.46: 5 residues within 4Å: Chain C: D.96, D.119, Y.120, R.121, L.122 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.119, C:Y.120 Water bridges: C:L.97 GOL.53: 5 residues within 4Å: Chain C: R.257, R.261 Chain D: E.269, A.270 Ligands: EDO.49 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.257, C:R.257, C:R.261, C:R.261 Water bridges: C:E.278 GOL.57: 9 residues within 4Å: Chain A: M.44 Chain C: F.14, A.17, I.18, M.21, A.40, L.41, M.44 Ligands: EDO.56 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.40 Water bridges: A:M.44 GOL.58: 6 residues within 4Å: Chain C: P.129, I.132, E.133, E.136, L.174, R.232 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.232 Water bridges: C:E.136, C:E.136 GOL.60: 4 residues within 4Å: Chain C: A.53, R.75, E.76, S.77 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.75, C:E.76, C:S.77 GOL.67: 4 residues within 4Å: Chain D: A.53, R.75, E.76, S.77 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.76, D:S.77 Water bridges: D:R.75 GOL.75: 8 residues within 4Å: Chain D: L.193, D.196, A.197, V.198, I.217, D.221, R.228, F.234 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.196, D:D.196, D:A.197, D:D.221, D:R.228

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

EDO.2: 5 residues within 4Å: Chain A: R.140, S.144, P.179, A.180, D.181 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.277, R.302 Chain B: M.309, M.310, G.312 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.8, P.9, D.10, M.11, S.295 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.308, M.309 Chain B: M.309 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: M.309, M.310, G.312 Chain B: L.277, R.302 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: A.53, A.74, R.75, E.76, S.77 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: R.140, S.144, P.179, A.180, D.181 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: R.8, P.9, D.10, S.295 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: A.27, F.219, T.222 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: I.7, K.12, L.15, E.16, G.209, F.210 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain A: E.269, A.270 Chain B: R.257, R.261 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain C: L.277, R.302, A.305 Chain D: D.273, M.309, M.310, G.312 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain C: R.50, A.109, L.110 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain C: R.140, S.144, P.179, A.180 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain C: A.201, S.202, A.205, F.206, R.257 Ligands: GOL.53 Ligand excluded by PLIP EDO.50: 8 residues within 4Å: Chain C: V.54, R.56, L.71, E.76, S.77, L.149, G.150, R.151 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain C: A.13, F.14, A.17, A.292 Ligands: CCN.11, GOL.57 Ligand excluded by PLIP EDO.59: 8 residues within 4Å: Chain C: P.24, T.25, L.26, M.29, T.213, S.216 Ligands: CCN.55, D8F.61 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain C: K.265 Chain D: D.262, K.265, A.266, E.269 Ligands: CCN.69 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain C: M.309, M.310, G.312 Chain D: L.277, R.302 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain D: S.145, P.146, S.147, E.148 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain D: R.140, S.144, P.179, A.180 Ligand excluded by PLIP EDO.72: 2 residues within 4Å: Chain D: A.80, T.152 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain C: E.269, A.270, G.271 Chain D: R.257, R.261 Ligand excluded by PLIP EDO.87: 7 residues within 4Å: Chain D: G.95, D.96, L.97, D.119, Y.120, R.121, L.122 Ligand excluded by PLIP

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

6NA.3: 7 residues within 4Å: Chain A: P.5, A.201, S.202, A.205, F.206, R.257, R.261 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.201, A:A.205, A:F.206 Water bridges: A:R.257, A:R.261 Salt bridges: A:R.257, A:R.261 6NA.17: 3 residues within 4Å: Chain A: K.265 Chain B: K.265, E.269 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:K.265, B:K.265, B:K.265 Salt bridges: A:K.265, B:K.265 6NA.54: 4 residues within 4Å: Chain C: K.308, M.309, L.311, G.312 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.308 Water bridges: C:K.308 6NA.77: 10 residues within 4Å: Chain D: L.26, A.27, M.29, T.30, L.31, A.34, P.124, F.219, A.223 Ligands: DMS.74 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.31, D:P.124, D:F.219, D:F.219 Water bridges: D:A.223 6NA.83: 9 residues within 4Å: Chain C: E.278, E.280 Chain D: A.243, P.244, P.245, T.246, R.272, D.273 Ligands: DMS.66 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.245, D:D.273, C:E.280 Hydrogen bonds: D:T.246, D:D.273, D:D.273 Salt bridges: D:R.272

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

DMS.6: 8 residues within 4Å: Chain A: V.54, R.56, L.71, E.76, S.77, L.149, G.150, R.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56, A:R.56, A:R.151 DMS.7: 3 residues within 4Å: Chain A: E.79, A.80, T.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.80 DMS.14: 5 residues within 4Å: Chain A: R.47, P.294, Q.297, G.298, E.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.47 Water bridges: A:Q.297 Salt bridges: A:E.301 DMS.15: 8 residues within 4Å: Chain A: L.193, D.196, A.197, V.198, I.217, D.221, R.228, F.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.228 Water bridges: A:D.221 Salt bridges: A:D.196, A:D.221 DMS.31: 1 residues within 4Å: Chain B: R.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.75 DMS.32: 5 residues within 4Å: Chain A: E.280 Chain B: T.241, A.242, R.272 Ligands: CCN.18 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:E.280 Hydrogen bonds: B:R.272, B:R.272 DMS.36: 3 residues within 4Å: Chain B: M.29, T.30, L.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.31 Water bridges: B:E.32 DMS.37: 4 residues within 4Å: Chain B: S.144, S.145, T.152 Ligands: DIO.24 No protein-ligand interaction detected (PLIP) DMS.42: 3 residues within 4Å: Chain B: I.55, R.56, N.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.56, B:R.56 DMS.63: 2 residues within 4Å: Chain C: R.272 Chain D: E.280 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:E.280 Hydrogen bonds: C:R.272, C:R.272 DMS.66: 4 residues within 4Å: Chain C: E.280 Chain D: A.242, R.272 Ligands: 6NA.83 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:E.280 Hydrogen bonds: D:R.272 DMS.74: 4 residues within 4Å: Chain D: M.29, T.30, L.31 Ligands: 6NA.77 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.31 DMS.78: 2 residues within 4Å: Chain D: R.75 Ligands: CCN.85 No protein-ligand interaction detected (PLIP)

24 x CCN: ACETONITRILE(Non-functional Binders)

CCN.8: 4 residues within 4Å: Chain A: L.15, E.16, A.19, G.209 Ligand excluded by PLIP CCN.9: 4 residues within 4Å: Chain A: G.62, P.63, A.64, G.65 Ligand excluded by PLIP CCN.10: 3 residues within 4Å: Chain A: P.124, E.125, P.127 Ligand excluded by PLIP CCN.11: 6 residues within 4Å: Chain A: F.14, A.17, M.44, A.292 Chain C: M.44 Ligands: EDO.56 Ligand excluded by PLIP CCN.13: 3 residues within 4Å: Chain A: I.236, L.237, H.240 Ligand excluded by PLIP CCN.18: 6 residues within 4Å: Chain A: E.278, E.280 Chain B: P.245, R.272, D.273 Ligands: DMS.32 Ligand excluded by PLIP CCN.27: 3 residues within 4Å: Chain B: T.30, E.32, E.33 Ligand excluded by PLIP CCN.29: 2 residues within 4Å: Chain B: G.298, R.302 Ligand excluded by PLIP CCN.30: 3 residues within 4Å: Chain B: R.70, D.98, H.101 Ligand excluded by PLIP CCN.33: 2 residues within 4Å: Chain B: G.23, T.25 Ligand excluded by PLIP CCN.34: 5 residues within 4Å: Chain B: Q.173, P.231, G.238, D.239 Ligands: CCN.38 Ligand excluded by PLIP CCN.38: 9 residues within 4Å: Chain B: S.172, Q.173, G.176, A.177, D.239, A.242, A.243, P.244 Ligands: CCN.34 Ligand excluded by PLIP CCN.51: 5 residues within 4Å: Chain C: R.56, L.58, S.59, W.141, E.148 Ligand excluded by PLIP CCN.52: 4 residues within 4Å: Chain C: T.25, A.27, E.28, A.215 Ligand excluded by PLIP CCN.55: 7 residues within 4Å: Chain C: I.18, E.208, G.209, F.210, V.211, T.213 Ligands: EDO.59 Ligand excluded by PLIP CCN.65: 5 residues within 4Å: Chain C: E.269 Chain D: R.257, D.258, R.261, D.262 Ligand excluded by PLIP CCN.69: 4 residues within 4Å: Chain C: K.265, E.269 Chain D: K.265 Ligands: EDO.62 Ligand excluded by PLIP CCN.73: 4 residues within 4Å: Chain D: E.79, A.80, G.81, P.82 Ligand excluded by PLIP CCN.76: 2 residues within 4Å: Chain D: L.174, R.232 Ligand excluded by PLIP CCN.80: 2 residues within 4Å: Chain D: A.40, M.44 Ligand excluded by PLIP CCN.81: 4 residues within 4Å: Chain D: A.49, D.98, H.101, N.102 Ligand excluded by PLIP CCN.82: 2 residues within 4Å: Chain D: P.61, W.141 Ligand excluded by PLIP CCN.84: 6 residues within 4Å: Chain D: L.175, G.176, P.179, A.180, P.183, V.184 Ligand excluded by PLIP CCN.85: 5 residues within 4Å: Chain D: R.75, R.78, E.79, D.112 Ligands: DMS.78 Ligand excluded by PLIP

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

D8F.16: 18 residues within 4Å: Chain A: L.26, Y.38, L.41, G.89, G.90, G.91, I.94, S.162, A.163, L.193, V.211, L.212, S.216, I.217, F.220, I.256, H.284, S.285 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.212, A:F.220 Hydrogen bonds: A:S.285 Water bridges: A:Y.38 Salt bridges: A:H.284 D8F.43: 18 residues within 4Å: Chain B: L.26, Y.38, L.41, G.89, G.90, G.91, I.94, S.162, A.163, L.193, V.211, L.212, S.216, I.217, F.220, I.256, H.284, S.285 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.26, B:Y.38, B:A.163, B:L.212, B:L.212, B:F.220 Water bridges: B:Y.38 Salt bridges: B:H.284 D8F.61: 19 residues within 4Å: Chain C: L.26, Y.38, L.41, G.89, G.90, G.91, I.94, S.162, A.163, L.193, V.211, L.212, S.216, I.217, F.220, I.256, H.284, S.285 Ligands: EDO.59 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.38, C:I.94, C:A.163, C:F.220 Hydrogen bonds: C:S.285 Salt bridges: C:H.284 D8F.88: 19 residues within 4Å: Chain D: L.26, Y.38, L.41, G.89, G.90, G.91, F.92, I.94, S.162, A.163, L.193, V.211, L.212, S.216, I.217, F.220, I.256, H.284, S.285 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.163 Salt bridges: D:H.284

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

SO4.19: 3 residues within 4Å: Chain A: A.242, R.272 Chain B: E.280 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:R.272, A:R.272, A:R.272, A:R.272 Salt bridges: A:R.272 Hydrogen bonds: B:E.280 SO4.20: 4 residues within 4Å: Chain A: A.53, R.75, E.76, S.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.76, A:S.77 Water bridges: A:R.75

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

DIO.24: 8 residues within 4Å: Chain B: S.145, P.146, S.147, L.149, G.150, R.151, T.152 Ligands: DMS.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.150

1 x BUA: butanoic acid(Non-covalent)

BUA.35: 4 residues within 4Å: Chain B: K.308, M.309, L.311, G.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.312

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

NPO.40: 8 residues within 4Å: Chain B: F.14, A.17, I.18, L.41, M.44, A.45, A.292 Ligands: NPO.41 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.41, B:A.45, B:A.292 pi-Stacking: B:F.14 NPO.41: 4 residues within 4Å: Chain B: A.17, M.21, M.44 Ligands: NPO.40 No protein-ligand interaction detected (PLIP) NPO.86: 5 residues within 4Å: Chain D: A.13, F.14, A.17, M.44, A.292 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.14 Hydrogen bonds: D:A.13

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

NA.64: 1 residues within 4Å: Chain C: D.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.98 Water bridges: C:D.119

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

2022-02-23

Peptides

Lipase: ABD
Lipase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

Lipase

Lipase

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