SMTL ID : 9j5b.1

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Dimethyl phthalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x TIK: dimethyl benzene-1,2-dicarboxylate(Non-covalent)

TIK.1: 19 residues within 4Å: Chain A: G.90, F.91, S.160, A.161, A.189, L.190, D.191, M.192, K.199, L.208, M.213, F.216, G.217, Y.220, L.221, L.256, E.259, H.284 Ligands: ACE.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.91, A:F.216 Water bridges: A:K.199 Salt bridges: A:K.199 TIK.2: 3 residues within 4Å: Chain A: L.43, Q.46, M.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.43, A:Q.46

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

EDO.3: 7 residues within 4Å: Chain A: K.126, G.217, E.218, L.221, R.222, T.223, P.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.217, A:R.222 EDO.4: 6 residues within 4Å: Chain A: R.78, F.79, V.110, A.303, L.306, E.307 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: T.59, V.60, V.61, W.140 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.61, A:W.140 Water bridges: A:V.61 EDO.7: 4 residues within 4Å: Chain A: H.6, R.257, R.278 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.257, A:R.257, A:R.278, A:R.278 Water bridges: A:E.252 EDO.8: 5 residues within 4Å: Chain A: H.81, K.151, P.245, I.309, D.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.151, A:D.310 EDO.9: 7 residues within 4Å: Chain A: G.58, T.59, V.60, I.69, W.140 Ligands: EDO.6, EDO.12 No protein-ligand interaction detected (PLIP) EDO.10: 9 residues within 4Å: Chain A: H.6, P.197, S.198, R.200, D.201, F.202, R.257, D.258 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.6, A:D.201, A:R.257, A:R.257 EDO.11: 7 residues within 4Å: Chain A: G.242, L.243, P.244, P.245, G.271, V.272, P.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.242, A:G.271 EDO.12: 8 residues within 4Å: Chain A: E.56, D.57, G.58, I.69, R.71, W.140, W.148 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.56, A:D.57, A:R.71 EDO.13: 4 residues within 4Å: Chain A: T.196, P.197, D.258, A.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.258 Water bridges: A:D.258, A:D.258, A:A.262 EDO.14: 4 residues within 4Å: Chain A: F.279, D.280, M.282, Q.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.280, A:Q.294 EDO.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain A: H.64, P.128, V.129, A.132, R.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64 EDO.17: 4 residues within 4Å: Chain A: L.28, S.29, L.30, A.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.30 Water bridges: A:S.29, A:A.31 EDO.18: 4 residues within 4Å: Chain A: V.61, T.62, T.63, D.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.63, A:D.136

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.5: 9 residues within 4Å: Chain A: G.88, G.89, G.90, S.160, A.161, L.208, L.256, H.284 Ligands: TIK.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.89, A:G.90, A:A.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verma, S. et al., Mechanistic and structural insights into EstS1 esterase: A potent broad-spectrum phthalate diester degrading enzyme. Structure (2025)

Release Date

2024-12-25

Peptides

Alpha/beta hydrolase fold-3 domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha/beta hydrolase fold-3 domain-containing protein

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