SMTL ID : 8daj.1

Structure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: D.136, H.183, A.184, R.185, K.302 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.184, A:K.302, A:K.302 EDO.2: 4 residues within 4Å: Chain A: G.269, H.270, A.271 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.270 EDO.3: 6 residues within 4Å: Chain A: C.78, F.82, M.155, Y.159, M.162 Ligands: IPA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.159 Water bridges: A:N.76 EDO.4: 6 residues within 4Å: Chain A: T.195, S.196, D.197, Y.198, Y.201, P.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.197 Water bridges: A:Y.201 EDO.7: 7 residues within 4Å: Chain A: Y.177, A.184, R.218, A.219, G.220, D.221 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.184 EDO.9: 2 residues within 4Å: Chain A: D.217, H.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.217 EDO.10: 3 residues within 4Å: Chain A: T.280, Y.281 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.281 EDO.11: 5 residues within 4Å: Chain A: A.184, R.185, D.221 Ligands: EDO.1, EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.184 EDO.13: 6 residues within 4Å: Chain A: H.206, A.232, Y.249, Y.251, K.262 Ligands: IPA.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.206, A:Y.251, A:Y.251, A:K.262 Water bridges: A:Y.249, A:Y.249 EDO.14: 1 residues within 4Å: Chain A: A.73 No protein-ligand interaction detected (PLIP)

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 7 residues within 4Å: Chain A: H.206, I.209, S.210, D.230, Y.251, K.262 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.206, A:D.230 Hydrogen bonds: A:H.206, A:Y.251, A:K.262 IPA.6: 2 residues within 4Å: Chain A: D.221, N.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.226 Water bridges: A:N.226 IPA.8: 9 residues within 4Å: Chain A: C.40, C.78, W.81, S.121, A.122, L.147, M.162, V.200 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.147, A:V.200 IPA.12: 5 residues within 4Å: Chain A: G.39, C.40, S.121, H.270, Y.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.281 Hydrogen bonds: A:C.40, A:S.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, G.M. et al., Bioplastic degradation by a polyhydroxybutyrate depolymerase from a thermophilic soil bacterium. Protein Sci. (2022)

Release Date

2023-02-15

Peptides

Esterase, PHB depolymerase family: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Esterase, PHB depolymerase family