5O2B

Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor PP-121

PDB DOI: https://doi.org/10.2210/pdb5O2B/pdb

Classification: STRUCTURAL GENOMICS
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-05-19 Released: 2017-06-28
Deposition Author(s): Pinkas, D.M., Bufton, J.C., Newman, J.A., Borkowska, O., Chalk, R., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor PP-121

Pinkas, D.M., Daubner, G.M., Bufton, J.C., Bartual, S.G., Sanvitale, C.E., Alessi, D.R., Bullock, A.

To be published.

Macromolecule Content

Total Structure Weight: 65.97 kDa
Atom Count: 4,330
Modelled Residue Count: 526
Deposited Residue Count: 570
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase WNK3	A, B	285	Homo sapiens	Mutation(s): 0 Gene Names: WNK3, KIAA1566, PRKWNK3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYP7 (Homo sapiens) Explore Q9BYP7 Go to UniProtKB: Q9BYP7
PHAROS: Q9BYP7 GTEx: ENSG00000196632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYP7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KS1 Query on KS1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C₁₇ H₁₇ N₇ NVRXTLZYXZNATH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.16	α = 90
b = 71.253	β = 103.88
c = 67.8	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 2.0: 2017-07-19
Changes: Atomic model, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2019-10-16
Changes: Data collection
Version 2.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations