9KQZ | pdb_00009kqz

Structural Basis for the Polymer-Protein Binding Mechanism of Polyvinyl Alcohol Esterase

PDB DOI: https://doi.org/10.2210/pdb9KQZ/pdb

Classification: HYDROLASE
Organism(s): Comamonas sp. NyZ500
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-27 Released: 2025-10-08
Deposition Author(s): Wu, Y.F., Xu, X.X., Yin, C.F., Wang, L.T., Zhou, N.Y., Zhou, J.
Funding Organization(s): National Key R&D Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.163 (Depositor), 0.164 (DCC)
R-Value Work:
0.142 (Depositor), 0.143 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural Basis for the Enzyme-Polymer Binding Mechanism of Poly(vinyl alcohol) Esterase

Wu, Y., Xu, X., Yin, C.F., Shen, Z., Wang, L., Zhou, N.Y., Zhou, J.

(2025) ACS Catal 15: 11194-11203

DOI: https://doi.org/10.1021/acscatal.5c01764

Macromolecule Content

Total Structure Weight: 42.88 kDa
Atom Count: 3,618
Modeled Residue Count: 391
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGNH/GDSL hydrolase family protein	A	403	Comamonas sp. NyZ500	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]