9Z6E: Apo LIMK1 mutant D460N

Crystal structure of apo LIMK1 mutant D460N. Determined by X-ray diffraction at 2.26 Å resolution. Released 22 Jul 2026.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,475
Mol. weight: 72.51 kDa
Released: 22 Jul 2026

Explore 9Z6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Z6E contains 29 α-helices and 28 β-strands across 2 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: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-334	3	1
α-helix	336-338	3
β-strand	339-348	10	1
β-strand	351-358	8	1
β-strand	364-369	6	1
α-helix	375-390	16
β-strand	396	1	2
α-helix	397-398	2
β-strand	399-403	5	1
β-strand	410-414	5	1
β-strand	420	1	2
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	3
β-strand	466-468	3	2
β-strand	474-476	3	2
β-strand	483-484	2	3
α-helix	518-521	4
α-helix	529-544	16
β-strand	555	1	4
β-strand	561	1	4
α-helix	563-569	7
α-helix	575-576	2
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-612	16
α-helix	618-632	15

Chain B: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-333	2	5
β-strand	344	1	5
β-strand	353-356	4	5
β-strand	365-369	5	5
α-helix	375-388	14
β-strand	396	1	6
α-helix	397-398	2
β-strand	399-402	4	5
β-strand	410-414	5	5
α-helix	415-416	2
β-strand	420	1	6
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	7
β-strand	466-468	3	6
β-strand	474-476	3	6
β-strand	483-484	2	7
α-helix	513-515	3
α-helix	518-521	4
α-helix	529-544	16
β-strand	555	1	8
β-strand	561	1	8
α-helix	563-569	7
α-helix	575-576	2
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-613	17
α-helix	618-631	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	A, B	protein	313	Homo sapiens	P53667 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9Z6E_1 LIM domain kinase 1 (chains A, B)
GRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKV
MRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASG
MAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRY
TVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFL
DRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRG
FWETYRRGESGLP

Primary citation

A covalent inhibitor targeting Cys-349 of LIMK1 confers selectivity over LIMK2. Patteson, J.B., Manolaridis, I., Hong, M.R. et al. J Biol Chem (2026) 302:113322-113322. DOI 10.1016/j.jbc.2026.113322 · PubMed

Other PDB entries of the same protein (UniProt P53667 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S95 1.65 Å, Crystal structure of the human LIMK1 kinase domain in complex with staurosporine
8AAU 1.74 Å, LIM Domain Kinase 1 (LIMK1) bound to LIMKi3
6WLY 1.9 Å, PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide
9Z6D 1.94 Å, Crystal structure of LIMK1 mutant D460N bound to small molecule inhibitor cLIMK1i
5HVJ 2.2 Å, Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP
5NXC 2.25 Å, LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736
5L6W 2.53 Å, Structure Of the LIMK1-ATPgammaS-CFL1 Complex
7ATS 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500127
7ATU 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500025
7B8W 2.8 Å, Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470
5HVK 3.5 Å, Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1

Browse structure collections

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