5NKP

Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide

• PDB DOI: https://doi.org/10.2210/pdb5NKP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2017-05-03 
• Deposition Author(s): Chen, Z., Sorrell, F.J., Pinkas, D.M., Williams, E., Mathea, S., Goubin, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Bountra, C., Bullock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide

Chen, Z., Sorrell, F.J., Pinkas, D.M., Williams, E., Mathea, S., Goubin, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Bountra, C., Bullock, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.99 kDa 
• Atom Count: 4,551 
• Modelled Residue Count: 596 
• Deposited Residue Count: 606 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like protein 3	A, B	292	Homo sapiens	Mutation(s): 0  Gene Names: KLHL3, KIAA1129
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UH77 (Homo sapiens) Explore Q9UH77  Go to UniProtKB:  Q9UH77
PHAROS:  Q9UH77 GTEx:  ENSG00000146021

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase WNK3	C [auth D], D [auth C]	11	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.66	α = 90
b = 169.72	β = 90
c = 123.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Chen, Z., Sorrell, F.J., Pinkas, D.M., Williams, E., Mathea, S., Goubin, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description