SMTL ID : 8ytz.1

The P185V variant of Kubu-PETase from Kutzneria buriramensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 5 residues within 4Å: Chain A: Q.4, D.230 Ligands: ACT.12, ACT.13, ACT.14 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions Metal complexes: A:D.230, A:D.230, ACT.12, ACT.13, ACT.14 ZN.2: 3 residues within 4Å: Chain A: D.203 Ligands: ACT.15, ACT.16 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:D.203, H2O.6 ZN.3: 3 residues within 4Å: Chain A: S.126, H.204 Ligands: ACT.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.126, A:H.204, H2O.6 ZN.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.5: 1 residues within 4Å: Chain A: D.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.17, A:D.17 ZN.6: 1 residues within 4Å: Chain A: E.198 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.198, A:E.198, H2O.5, H2O.7, H2O.7 ZN.7: 1 residues within 4Å: Chain A: D.81 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.81, H2O.1, H2O.3 ZN.8: 2 residues within 4Å: Chain A: D.94, K.138 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, H2O.1 ZN.9: 3 residues within 4Å: Chain A: D.3, T.46, R.119 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.46, H2O.1, H2O.5, H2O.5, H2O.5

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

1PE.10: 9 residues within 4Å: Chain A: A.11, I.14, T.15, T.213, R.216, G.238, F.239, A.240, V.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:A.240 1PE.11: 5 residues within 4Å: Chain A: V.57, S.58, T.82, S.84, G.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.82 Water bridges: A:G.85, A:G.85

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

ACT.12: 6 residues within 4Å: Chain A: Q.4, D.230, R.231 Ligands: ZN.1, ACT.13, ACT.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.4 ACT.13: 5 residues within 4Å: Chain A: Q.4, D.230 Ligands: ZN.1, ACT.12, ACT.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.4 Water bridges: A:D.230 ACT.14: 4 residues within 4Å: Chain A: D.230 Ligands: ZN.1, ACT.12, ACT.13 No protein-ligand interaction detected (PLIP) ACT.15: 4 residues within 4Å: Chain A: D.203, F.205 Ligands: ZN.2, ACT.16 No protein-ligand interaction detected (PLIP) ACT.16: 5 residues within 4Å: Chain A: D.203, F.205, T.208 Ligands: ZN.2, ACT.15 No protein-ligand interaction detected (PLIP) ACT.17: 6 residues within 4Å: Chain A: F.56, S.58, S.126, H.204, F.205 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.205 Hydrogen bonds: A:F.56, A:S.58, A:S.126 Salt bridges: A:H.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seo, H. et al., Landscape profiling of PET depolymerases using a natural sequence cluster framework. Science (2025)

Release Date

2025-01-15

Peptides

Dienelactone hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dienelactone hydrolase