Bicyclic INCYPRO Pseudomonas fluorescens esterase

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Covalent bicyclization of protein complexes yields durable quaternary structures.

Hutchins, G.H.Kiehstaller, S.Poc, P.Lewis, A.H.Oh, J.Sadighi, R.Pearce, N.M.Ibrahim, M.Drienovska, I.Rijs, A.M.Neubacher, S.Hennig, S.Grossmann, T.N.

(2024) Chem 10: 615-627

  • DOI: https://doi.org/10.1016/j.chempr.2023.10.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Proteins are essential biomolecules and central to biotechnological applications. In many cases, assembly into higher-order structures is a prerequisite for protein function. Under conditions relevant for applications, protein integrity is often challenged, resulting in disassembly, aggregation, and loss of function. The stabilization of quaternary structure has proven challenging, particularly for trimeric and higher-order complexes, given the complexity of involved inter- and intramolecular interaction networks. Here, we describe the chemical bicyclization of homotrimeric protein complexes, thereby increasing protein resistance toward thermal and chemical stress. This approach involves the structure-based selection of cross-linking sites, their variation to cysteine, and a subsequent reaction with a triselectrophilic agent to form a protein assembly with bicyclic topology. Besides overall increased stability, we observe resistance toward aggregation and greatly prolonged shelf life. This bicyclization strategy gives rise to unprecedented protein chain topologies and can enable new biotechnological and biomedical applications.

  • Organizational Affiliation

    Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, the Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
280Pseudomonas fluorescensMutation(s): 2 
Gene Names: estF
EC: (PDB Primary Data), 1 (PDB Primary Data)
Find proteins for P22862 (Pseudomonas fluorescens)
Explore P22862 
Go to UniProtKB:  P22862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22862
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZIZ (Subject of Investigation/LOI)
Query on ZIZ

Download Ideal Coordinates CCD File 
CA [auth G]
EA [auth G]
JA [auth J]
KA [auth J]
P [auth A]
CA [auth G],
EA [auth G],
JA [auth J],
KA [auth J],
P [auth A],
Q [auth A],
U [auth D],
V [auth D],
VA [auth M],
WA [auth M]
C15 H21 I3 N6 O6
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
FA [auth H]
GA [auth I]
AA [auth F],
BA [auth F],
DA [auth G],
FA [auth H],
GA [auth I],
HA [auth J],
IA [auth J],
LA [auth K],
MA [auth K],
NA [auth K],
OA [auth K],
PA [auth L],
QA [auth L],
R [auth A],
RA [auth L],
S [auth B],
SA [auth M],
T [auth B],
TA [auth M],
UA [auth M],
W [auth D],
X [auth D],
XA [auth O],
Y [auth D],
Z [auth E]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.8α = 90
b = 146.25β = 122.63
c = 154.59γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union839088
Netherlands Organisation for Scientific Research (NWO)Netherlands18617

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-02-21
    Changes: Database references