8AAU: LIM Domain Kinase 1

LIM Domain Kinase 1 (LIMK1) bound to LIMKi3. Determined by X-ray diffraction at 1.74 Å resolution. Released 10 Aug 2022.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,432
Mol. weight: 36.8 kDa
Ligands: MG, LH0
Released: 10 Aug 2022

Explore 8AAU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AAU contains 17 α-helices and 16 β-strands across 1 chain. 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 L: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	329-331	3
β-strand	332-334	3	1
α-helix	336-338	3
β-strand	339-347	9	1
β-strand	351-358	8	1
β-strand	364-370	7	1
α-helix	375-389	15
β-strand	396	1	2
α-helix	397-398	2
β-strand	399-405	7	1
β-strand	408-414	7	1
β-strand	418-420	3	2
α-helix	421-427	7
α-helix	434-453	20
β-strand	456-457	2	3
β-strand	466-469	4	2
β-strand	474-476	3	2
β-strand	483-484	2	3
β-strand	505	1	4
α-helix	507-509	3
α-helix	513-515	3
α-helix	518-521	4
β-strand	526	1	4
α-helix	529-544	16
β-strand	555	1	5
β-strand	561	1	5
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	618-633	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	L	protein	310	Homo sapiens	P53667 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8AAU_1 LIM domain kinase 1 (chains L)
SMPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKV
MRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASG
MAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRY
TVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFL
DRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRG
FWETYRRGES

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
LH0	~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3…	C17 H14 Cl2 F2 N4 O S	1

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. Hanke, T., Mathea, S., Woortman, J. et al. J Med Chem (2022) 65:13264-13287. DOI 10.1021/acs.jmedchem.2c01106 · 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
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
9Z6E 2.26 Å, Crystal structure of apo LIMK1 mutant D460N
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

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