30OP | pdb_000030op

Putative Polyurethane Degrading Amidase Bound to Fragment VT00048

• PDB DOI: https://doi.org/10.2210/pdb30OP/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas spermidinifaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-05-06 Released: 2026-11-04 
• Deposition Author(s): Bicer, D., Otzen, D.E., Morth, J.P., Thirup, S.S.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.305 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.289 (Depositor) 

Starting Model: in silico

Literature

Fragment-based active-site exploration of urethane hydrolases reveals a diversity of urethane binding modes

Bicer, D., Kochubei, D., Graham, R., Pena-Diaz, S., Rotilio, L., Villadsen, N.L., Sommerfeldt, A., Johansen, M.B., Sandahl, A., Thirup, S.S., Morth, J.P., Otzen, D.E.

(2026) Acta Crystallogr D Biol Crystallogr 

• DOI: https://doi.org/10.1107/S2059798326010624

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.07 kDa 
• Atom Count: 7,000 
• Modeled Residue Count: 846 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase	A, B [auth C]	433	Sphingomonas spermidinifaciens	Mutation(s): 0  Gene Names: COC42_04005
UniProt
Find proteins for A0A2A4B7C5 (Sphingomonas spermidinifaciens) Explore A0A2A4B7C5  Go to UniProtKB:  A0A2A4B7C5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I14 (Subject of Investigation/LOI)	C [auth A], E [auth C]	6-chloranyl-3~{H}-1,3-benzoxazol-2-one C7 H4 Cl N O2 MATCZHXABVLZIE-UHFFFAOYSA-N
MG	D [auth A], F [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.305 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.289 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.26	α = 90
b = 111.26	β = 90
c = 436.19	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Bicer, D., Otzen, D.E., Morth, J.P., Thirup, S.S.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF22OC0072891

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release