9KR3 | pdb_00009kr3

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

PDB DOI: https://doi.org/10.2210/pdb9KR3/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: 1.78 Å
R-Value Free:
0.177 (Depositor), 0.179 (DCC)
R-Value Work:
0.157 (Depositor), 0.162 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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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: 43.16 kDa
Atom Count: 3,615
Modeled Residue Count: 391
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGNH/GDSL hydrolase family protein	A	403	Comamonas sp. NyZ500	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EGL (Subject of Investigation/LOI) Query on A1EGL 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]	[(2S,4S,6S,8S,10R,12R,14R,16R,18R,20R)-12-acetyloxy-2,4,6,10,14,16,18,20,22-nonakis(oxidanyl)docosan-8-yl] ethanoate C₂₆ H₅₀ O₁₃ KNZHZBPEWADAET-WIIBHWIMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.177 (Depositor), 0.179 (DCC)
R-Value Work: 0.157 (Depositor), 0.162 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.79	α = 90
b = 164.79	β = 90
c = 164.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Key R&D Program of China	China	2021YFA0909500

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.