5QUB | pdb_00005qub

HumRadA1.2 soaked with napht-2,3-diol for 30 seconds at 20 mM

PDB DOI: https://doi.org/10.2210/pdb5QUB/pdb
Deposition Group: G_1002113 | Explore G_1002113
Entry: 5QUB supersedes: 6TXY

Classification: DNA BINDING PROTEIN
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-27 Released: 2021-03-03
Deposition Author(s): Marsh, M., Hyvonen, M.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Optimisation of crystal forms for structure-guided drug discovery

Brear, P.B., Fischer, G., Rocaboy, R., Marsh, M., Rossmann, M., Pantelejevs, T., Wagstaff, J., Blaszczyk, B.K.

To be published.

Macromolecule Content

Total Structure Weight: 25.54 kDa
Atom Count: 2,132
Modeled Residue Count: 222
Deposited Residue Count: 229
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RadA	A	229	Pyrococcus furiosus	Mutation(s): 0
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O74036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D48 (Subject of Investigation/LOI) Query on D48 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]	naphthalene-2,3-diol C₁₀ H₈ O₂ JRNGUTKWMSBIBF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.989	α = 90
b = 72.823	β = 90
c = 40.411	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

This entry supersedes: 6TXY

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	080083/Z/06/Z 91050/Z/10/Z

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2021-05-12
Changes: Structure summary
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.