8A2C

The crystal structure of the S178A mutant of PET40, a PETase enzyme from an unclassified Amycolatopsis

PDB DOI: https://doi.org/10.2210/pdb8A2C/pdb

Classification: HYDROLASE
Organism(s): unclassified Amycolatopsis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-03 Released: 2023-06-14
Deposition Author(s): Costanzi, E., Applegate, V., Port, A., Smits, S.H.J.
Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.179
R-Value Work: 0.146
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The metagenome-derived esterase PET40 hydrolyses polyethylene terephthalate (PET) and is well conserved in the GC-rich gram-positives Amycolatopsis and Streptomyces

Zhang, H., Dierkes, R., Perez-Garcia, P., Applegate, V., Costanzi, E., Partus, K., Gurschke, M., Schmeisser, C., Smits, S.H.J., Chow, J., Streit, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 60.38 kDa
Atom Count: 4,745
Modelled Residue Count: 535
Deposited Residue Count: 556
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PET40 S178A	A, B	278	unclassified Amycolatopsis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B]	C [auth A], Q [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain U [auth B]	O [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain U [auth B] Interactions & Density Focus chain O [auth A] Focus chain U [auth B]