5NKP | pdb_00005nkp

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UH77
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.247 (Depositor), 0.247 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary