SMTL ID : 8z91.1

Soil metagenomic-derived esterase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: G.52, Y.53, S.140, M.141, C.166, F.203, H.310 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.203 Hydrogen bonds: A:Y.53, A:M.141 Salt bridges: A:H.310 ACT.7: 6 residues within 4Å: Chain B: G.52, Y.53, S.140, M.141, C.166, F.203 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.203 Hydrogen bonds: B:Y.53, B:M.141 ACT.10: 7 residues within 4Å: Chain C: G.52, Y.53, S.140, M.141, C.166, F.203, H.310 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.203 Hydrogen bonds: C:Y.53, C:M.141 Salt bridges: C:H.310 ACT.16: 6 residues within 4Å: Chain D: G.52, Y.53, S.140, M.141, C.166, F.203 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.203 Hydrogen bonds: D:Y.53, D:M.141

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

PEG.2: 1 residues within 4Å: Chain A: W.92 No protein-ligand interaction detected (PLIP) PEG.3: 6 residues within 4Å: Chain A: A.70, M.71, E.74, M.75, R.80, E.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80 Water bridges: A:E.74 PEG.8: 5 residues within 4Å: Chain B: P.197, S.199, L.200, F.203 Chain D: K.276 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:P.197, D:K.276 PEG.11: 1 residues within 4Å: Chain C: W.92 No protein-ligand interaction detected (PLIP) PEG.12: 6 residues within 4Å: Chain C: A.70, M.71, E.74, M.75, R.80, E.319 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.80 Water bridges: C:E.74 PEG.17: 5 residues within 4Å: Chain B: K.276 Chain D: P.197, S.199, L.200, F.203 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:P.197, B:K.276

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 12 residues within 4Å: Chain A: Y.161, M.301, F.302, E.303, R.321, F.325 Chain B: Y.161, M.301, F.302, E.303, R.321, F.325 No protein-ligand interaction detected (PLIP) 1PE.13: 12 residues within 4Å: Chain C: Y.161, M.301, F.302, E.303, R.321, F.325 Chain D: Y.161, M.301, F.302, E.303, R.321, F.325 No protein-ligand interaction detected (PLIP)

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

SO4.5: 2 residues within 4Å: Chain A: K.58, S.62 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.58 Salt bridges: A:K.58 SO4.6: 4 residues within 4Å: Chain A: L.330, D.331, F.332, T.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.331, A:F.332, A:T.333 Water bridges: A:Q.82 SO4.9: 4 residues within 4Å: Chain B: S.179, K.183 Chain D: R.283, I.284 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.179 Water bridges: B:K.183, B:E.201 Salt bridges: B:K.183, D:R.283 SO4.14: 2 residues within 4Å: Chain C: K.58, S.62 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.58 Salt bridges: C:K.58 SO4.15: 4 residues within 4Å: Chain C: L.330, D.331, F.332, T.333 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.331, C:F.332, C:T.333 Water bridges: C:Q.82, C:D.331, C:D.331 SO4.18: 4 residues within 4Å: Chain B: R.283, I.284 Chain D: S.179, K.183 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.179 Water bridges: D:K.183 Salt bridges: D:K.183, B:R.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W., Discovery and characterization of a novel bottle-grade PET depolymerase with a BON domain-containing protein. To Be Published

Release Date

2024-12-25

Peptides

Esterase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Esterase