SMTL ID : 9hl5.1

Crystal structure of halo-tolerant PETase from marine metagenome (HaloPETase1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: T.255, D.256, N.257, D.258 Ligands: GOL.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.255, A:N.257, A:N.257 Water bridges: A:D.258 GOL.2: 9 residues within 4Å: Chain A: S.1, N.3, N.12, V.22, S.23, S.24, F.25, D.239, S.241 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.1, A:S.1, A:N.3, A:N.12, A:S.241 Water bridges: A:V.22 GOL.3: 14 residues within 4Å: Chain A: N.3, P.4, N.12, P.13, D.14, T.15, G.16, G.21, V.22, R.233, D.238, D.239, A.240, S.241 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.3, A:D.14, A:G.16, A:A.240, A:S.241 Water bridges: A:V.22, A:R.233 GOL.4: 6 residues within 4Å: Chain A: R.263, K.264, G.265, I.266, A.268 Ligands: GOL.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.266, A:I.266 Water bridges: A:A.268 GOL.5: 4 residues within 4Å: Chain A: G.222, D.223, R.225 Ligands: GOL.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.225, A:R.225 Water bridges: A:S.26, A:G.222 GOL.11: 4 residues within 4Å: Chain A: D.14, G.18, N.53, L.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.14, A:N.53 Water bridges: A:D.14 GOL.14: 8 residues within 4Å: Chain A: G.10, S.11, N.12, P.20, G.21, V.22, S.30 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.12, A:N.12, A:S.30 Water bridges: A:S.30 GOL.18: 7 residues within 4Å: Chain A: T.66, N.94, G.96, T.97, Q.135, L.162, G.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.94, A:Q.135 GOL.19: 9 residues within 4Å: Chain A: T.66, S.134, Q.135, Y.158, L.162, I.186, A.187, H.214 Ligands: PGE.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.66 GOL.20: 8 residues within 4Å: Chain A: Y.158, I.160, T.185, I.186, A.187, S.188, L.191, N.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.185, A:I.186, A:S.188, A:N.192 GOL.22: 4 residues within 4Å: Chain A: Q.145, D.146, Y.147, N.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.147, A:N.171 Water bridges: A:Q.145 GOL.27: 6 residues within 4Å: Chain A: S.249, C.254, V.261, R.263 Ligands: GOL.4, EDO.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.254, A:R.263, A:R.263 Water bridges: A:L.253, A:C.254, A:V.261 GOL.28: 7 residues within 4Å: Chain A: S.26, D.223, G.226, P.227, L.253, W.259 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.26, A:D.223, A:D.223, A:D.223, A:G.226 Water bridges: A:S.26 GOL.29: 4 residues within 4Å: Chain A: T.255, N.257 Ligands: GOL.1, EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.257, A:N.257

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 9 residues within 4Å: Chain A: D.28, G.29, S.30, F.31, A.32, T.33, S.48, E.78, S.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.33, A:T.33 PGE.15: 4 residues within 4Å: Chain A: T.110, N.113, R.114 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113 PGE.23: 8 residues within 4Å: Chain A: S.26, A.27, D.28, G.75, E.78, H.79, S.220, R.225 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.28, A:S.220 Water bridges: A:S.26, A:D.28 PGE.25: 4 residues within 4Å: Chain A: T.97, Q.99, D.100, N.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.97 Water bridges: A:Q.99 PGE.30: 13 residues within 4Å: Chain A: G.65, T.66, T.67, A.68, T.72, Y.73, H.133, S.134, I.186, H.214, F.215, V.218 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.67, A:T.67

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 10 residues within 4Å: Chain A: N.126, R.127, K.150, V.151, N.173, G.174, P.175, H.235, L.236 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.126, A:K.150, A:N.173, A:N.173

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

PEG.8: 5 residues within 4Å: Chain A: Y.234, E.243, Y.247, G.248, N.267 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.243, A:N.267 PEG.9: 7 residues within 4Å: Chain A: T.190, L.191, L.194, P.195, N.198, R.199 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.198 Water bridges: A:L.191 PEG.10: 7 residues within 4Å: Chain A: L.125, N.126, I.128, Y.147, R.148, K.150 Ligands: PG4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.150

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

EDO.12: 6 residues within 4Å: Chain A: R.46, S.48, T.49, L.50, T.118, K.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.50, A:K.122 EDO.13: 12 residues within 4Å: Chain A: T.159, I.160, H.164, S.166, Q.169, L.191, N.192, P.195, V.196, R.199 Ligands: PEG.9, EDO.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.159, A:T.159, A:Q.169, A:R.199, A:R.199 Water bridges: A:L.191 EDO.16: 7 residues within 4Å: Chain A: T.159, I.160, G.161, H.164, N.165, S.166 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.166, A:S.166 EDO.17: 6 residues within 4Å: Chain A: S.249, N.250, C.254, T.255 Ligands: GOL.27, GOL.29 No protein-ligand interaction detected (PLIP) EDO.21: 7 residues within 4Å: Chain A: V.22, S.23, S.24, D.28, G.29, S.30 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.23 Water bridges: A:G.10, A:S.23, A:S.30, A:S.30 EDO.24: 4 residues within 4Å: Chain A: R.114, S.115, T.116 Ligands: PGE.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.115, A:S.115, A:S.115, A:S.115 EDO.26: 5 residues within 4Å: Chain A: M.142, Q.145, N.165, S.167, S.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.145 Water bridges: A:Q.145, A:N.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turak, O. et al., A third type of PETase from the marine Halopseudomonas lineage. Protein Sci. (2025)

Release Date

2025-10-01

Peptides

Alpha/beta hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha/beta hydrolase