9KR0 | pdb_00009kr0

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

PDB DOI: https://doi.org/10.2210/pdb9KR0/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: 1.80 Å
R-Value Free:
0.160 (Depositor), 0.160 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

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

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: 42.72 kDa
Atom Count: 3,437
Modeled Residue Count: 391
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.160 (Depositor), 0.160 (DCC)
R-Value Work: 0.153 (Depositor), 0.153 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164	α = 90
b = 164	β = 90
c = 164	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

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

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.