6XUJ | pdb_00006xuj

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Optimising crystallographic systems for structure-guided drug discovery

Brear, P.B., Marsh, M., Hyvonen, M.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O1E (Subject of Investigation/LOI) Query on O1E 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]	5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine C₁₃ H₁₄ N₄ S UEBXWPXCTRZFCZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.168 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.