7B8W: LIM domain kinase 1

Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Mar 2022.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,652
Mol. weight: 146.59 kDa
Ligands: T3B
Released: 2 Mar 2022

Explore 7B8W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B8W contains 59 α-helices and 54 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	336-338	3
β-strand	339-345	7	1
β-strand	353-358	6	1
β-strand	364-369	6	1
α-helix	375-388	14
β-strand	393	1	2
β-strand	396	1	2
α-helix	397-398	2
β-strand	399-405	7	1
β-strand	408-414	7	1
α-helix	415-417	3
β-strand	418-420	3	2
α-helix	421-426	6
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	484-485	2	3
α-helix	513-515	3
α-helix	518-522	5
α-helix	530-544	15
β-strand	555	1	4
β-strand	561	1	4
α-helix	563-569	7
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-613	17
α-helix	619-629	11

Chain B: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	336-338	3
β-strand	339-340	2	5
β-strand	344-345	2	5
β-strand	353-358	6	5
β-strand	364-369	6	5
α-helix	375-388	14
β-strand	396	1	6
α-helix	397-398	2
β-strand	399-405	7	5
β-strand	408-414	7	5
β-strand	418-420	3	6
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	7
β-strand	466-469	4	6
β-strand	474-476	3	6
β-strand	484-485	2	7
α-helix	513-515	3
α-helix	518-522	5
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	595-596	2
α-helix	597-613	17
α-helix	619-629	11

Chain C: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	336-338	3
β-strand	339-345	7	9
β-strand	353-358	6	9
β-strand	364-369	6	9
α-helix	375-388	14
β-strand	396	1	10
α-helix	397-398	2
β-strand	399-405	7	9
β-strand	408-414	7	9
α-helix	415-417	3
β-strand	418-420	3	10
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	11
β-strand	466-469	4	10
β-strand	474-476	3	10
β-strand	484-485	2	11
α-helix	518-522	5
α-helix	530-544	15
β-strand	555	1	12
β-strand	561	1	12
α-helix	563-569	7
α-helix	576	1
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-613	17
α-helix	619-629	11

Chain D: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	336-338	3
β-strand	339-344	6	13
β-strand	353-358	6	13
β-strand	364-369	6	13
α-helix	375-383	9
α-helix	385-390	6
β-strand	396	1	14
α-helix	397-398	2
β-strand	399-405	7	13
β-strand	408-414	7	13
β-strand	418-420	3	14
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	15
β-strand	466-469	4	14
β-strand	474-476	3	14
β-strand	484-485	2	15
α-helix	518-521	4
α-helix	530-544	15
β-strand	555	1	16
β-strand	561	1	16
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	619-631	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	A, B, C, D	protein	310	Homo sapiens	P53667 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7B8W_1 LIM domain kinase 1 (chains A, B, C, D)
SMPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKV
MRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASG
MAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRY
TVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFL
DRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRG
FWETYRRGES

Ligands and cofactors

ID	Name	Formula	Copies
T3B	2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]c…	C30 H31 N5 O5 S2	4

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

Primary citation

Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470. Lee, H., Yosaatmadja, Y., Burgess-Brown, N.A. et al. To be published.

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
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
5HVK 3.5 Å, Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1

Browse structure collections

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