5NKP: Human KLHL3 Kelch domain

Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,551
Mol. weight: 65.99 kDa
Ligands: CIT
Released: 3 May 2017

Explore 5NKP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NKP contains 12 α-helices and 80 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	301-306	6	1
β-strand	309	1	2
β-strand	313	1	2
β-strand	317-321	5	1
β-strand	326-329	4	1
α-helix	331-333	3
β-strand	338	1	3
β-strand	341-345	5	3
β-strand	348-355	8	3
β-strand	360-368	9	3
β-strand	373-376	4	3
α-helix	378-380	3
β-strand	385	1	4
β-strand	388-392	5	5
β-strand	395-399	5	5
β-strand	402	1	4
β-strand	407	1	4
β-strand	411-415	5	5
β-strand	420-423	4	5
α-helix	425-427	3
β-strand	432	1	6
β-strand	435-438	4	6
β-strand	443-450	8	6
β-strand	455-464	10	6
β-strand	469-472	4	6
α-helix	474-476	3
β-strand	481	1	7
β-strand	484-488	5	8
β-strand	491-495	5	8
β-strand	498-499	2	7
β-strand	502-503	2	7
β-strand	507-511	5	8
β-strand	516-519	4	8
α-helix	521-523	3
β-strand	528	1	9
β-strand	531-535	5	10
β-strand	538-542	5	10
β-strand	545	1	9
β-strand	550	1	9
β-strand	551	1	11
β-strand	554-558	5	10
β-strand	563-566	4	10
β-strand	575	1	11
β-strand	576	1	2
β-strand	579-584	6	1

Chain B: 5 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	300	1
β-strand	301-306	6	12
β-strand	309	1	13
β-strand	313	1	13
β-strand	317-321	5	12
β-strand	326-329	4	12
α-helix	331-333	3
β-strand	338	1	14
β-strand	341-345	5	15
β-strand	348-352	5	15
β-strand	355	1	14
β-strand	360	1	14
β-strand	364-368	5	15
β-strand	373-377	5	15
β-strand	385	1	16
β-strand	388-391	4	16
β-strand	395-402	8	16
β-strand	407-415	9	16
β-strand	420-423	4	16
α-helix	425-427	3
β-strand	432	1	17
β-strand	435-439	5	18
β-strand	442-446	5	18
β-strand	449-450	2	17
β-strand	455-456	2	17
β-strand	460-464	5	18
β-strand	469-472	4	18
α-helix	474-476	3
β-strand	481	1	19
β-strand	484-487	4	20
β-strand	492-495	4	20
β-strand	498-499	2	19
β-strand	502-503	2	19
β-strand	507-511	5	20
β-strand	516-519	4	20
α-helix	521-523	3
β-strand	528	1	21
β-strand	531-535	5	22
β-strand	538-542	5	22
β-strand	545	1	21
β-strand	550	1	21
β-strand	554-558	5	22
β-strand	563-566	4	22
β-strand	576	1	13
β-strand	579-584	6	12

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	542-545	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kelch-like protein 3	A, B	protein	292	Homo sapiens	Q9UH77 (AlphaFold model)
Serine/threonine-protein kinase WNK3	C, D	protein	11	Homo sapiens	Q9BYP7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5NKP_1 Kelch-like protein 3 (chains A, B)
SMSLPKVMIVVGGQAPKAIRSVECYDFEEDRWDQIAELPSRRCRAGVVFMAGHVYAVGGF
NGSLRVRTVDVYDGVKDQWTSIASMQERRSTLGAAVLNDLLYAVGGFDGSTGLASVEAYS
YKTNEWFFVAPMNTRRSSVGVGVVEGKLYAVGGYDGASRQCLSTVEQYNPATNEWIYVAD
MSTRRSGAGVGVLSGQLYATGGHDGPLVRKSVEVYDPGTNTWKQVADMNMCRRNAGVCAV
NGLLYVVGGDDGSCNLASVEYYNPVTDKWTLLPTNMSTGRSYAGVAVIHKSL

Sequence of entity 2 (C, D), FASTA

>5NKP_2 Serine/threonine-protein kinase WNK3 (chains C, D)
ECEETEVDQHV

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide. Chen, Z., Sorrell, F.J., Pinkas, D.M. et al. To be published.

Other PDB entries of the same protein (UniProt Q9UH77 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CH9 1.84 Å, Crystal structure of the human KLHL3 Kelch domain in complex with a WNK4 peptide
4HXI 3.51 Å, Crystal structure of KLHL3/Cul3 complex

Browse structure collections

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