6XUJ

HumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine in P21212

• PDB DOI: https://doi.org/10.2210/pdb6XUJ/pdb

• Classification: RECOMBINATION
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-01-20 Released: 2021-03-03 
• Deposition Author(s): Marsh, M.E., Scott, D.E., Hyvonen, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.205 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Optimising crystallographic systems for structure-guided drug discovery

Brear, P.B., Marsh, M., Hyvonen, M.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 25.86 kDa 
• Atom Count: 2,089 
• Modelled Residue Count: 224 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein RadA	A	231	Pyrococcus furiosus DSM 3638	Mutation(s): 5  Gene Names: radA, PF1926
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O74036  Go to UniProtKB:  O74036

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O1E (Subject of Investigation/LOI)	C [auth A]	5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine C13 H14 N4 S UEBXWPXCTRZFCZ-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.205 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.453	α = 90
b = 73.211	β = 90
c = 40.793	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Marsh, M.E., Scott, D.E., Hyvonen, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	080083/Z/06/Z

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description