9DYS | pdb_00009dys

X-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature bound to tetraethylene glycol

PDB DOI: https://doi.org/10.2210/pdb9DYS/pdb

Classification: HYDROLASE
Organism(s): Alphaproteobacteria bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-14 Released: 2025-01-29
Deposition Author(s): Capra, N., Meilleur, F.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.172 (Depositor), 0.180 (DCC)
R-Value Work:
0.151 (Depositor), 0.158 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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Literature

Identification and characterization of substrate- and product-selective nylon hydrolases

Drufva, E.E., Cahill, J.F., Saint-Vincent, P.M., Williams, A.N., Bocharova, V., Capra, N., Meilleur, F., Carper, D.L., Bourgery, C., Miyazaki, K., Yonemura, M., Shiraishi, Y., Parks, J.M., Zhou, M., Dishner, I.T., Foster, J.C., Koehler, S.J., Valentino, H.R., Sedova, A., Kertesz, V., Vasileva, D.P., Hochanadel, L.H., Figg, C.A., Negoro, S., Kato, D.I., Chen, S.H., Michener, J.K.

(2025) Chem Catal 5: 101418

DOI: https://doi.org/10.1016/j.checat.2025.101418

Macromolecule Content

Total Structure Weight: 63.12 kDa
Atom Count: 4,609
Modeled Residue Count: 605
Deposited Residue Count: 610
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(hexamethylene adipamide) hydrolase	A, B	305	Alphaproteobacteria bacterium	Mutation(s): 0 Gene Names: EPN97_01225
UniProt
Find proteins for A0ACD6BAK9 (Alphaproteobacteria bacterium) Explore A0ACD6BAK9 Go to UniProtKB: A0ACD6BAK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.172 (Depositor), 0.180 (DCC)
R-Value Work: 0.151 (Depositor), 0.158 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.879	α = 90
b = 96.511	β = 90
c = 105.188	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC05-00OR22725

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release
Version 1.1: 2026-06-03
Changes: Database references

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