9R40 | pdb_00009r40

HaloTag bound to compound MRC71

• PDB DOI: https://doi.org/10.2210/pdb9R40/pdb

• Classification: LIGASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-06 Released: 2025-10-08 
• Deposition Author(s): Luptak, J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.233 (DCC) 

Starting Model: experimental

Literature

Development of TRIM21 PROTAC molecules

Luptak, J., James, L.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 35.66 kDa 
• Atom Count: 2,459 
• Modeled Residue Count: 293 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	306	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 0  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JC1 (Subject of Investigation/LOI)	C [auth A]	(2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(2-methoxyphenyl)propanoyl]-~{N}-[(2~{R})-1-[2-[2-[2-[2-(6-chloranylhexoxy)ethoxy]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]-4-cyclohexyl-pyrrolidine-2-carboxamide C43 H66 Cl N5 O8 NRBOBAOLCBJHID-ZACWFTDDSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.233 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.797	α = 90
b = 62.797	β = 90
c = 163.274	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Luptak, J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

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