7ATU: The LIMK1 Kinase Domain

The LIMK1 Kinase Domain Bound To LIJTF500025. Determined by X-ray diffraction at 2.8 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,875
Mol. weight: 145.9 kDa
Ligands: RXN
Released: 23 Dec 2020

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

Secondary structure: helices and β-sheets

7ATU contains 51 α-helices and 50 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: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	343	1	1
α-helix	348-350	3
β-strand	354-357	4	1
β-strand	364-369	6	1
α-helix	375-389	15
β-strand	396	1	2
β-strand	399-403	5	1
β-strand	410-414	5	1
β-strand	419-420	2	2
α-helix	421-426	6
α-helix	434-453	20
β-strand	457	1	3
β-strand	466-468	3	2
β-strand	474-476	3	2
β-strand	484	1	3
α-helix	518-521	4
α-helix	529-543	15
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	595-596	2
α-helix	597-613	17
α-helix	619-629	11

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	336-338	3
β-strand	339-344	6	5
α-helix	348-350	3
β-strand	354-358	5	5
β-strand	364-369	6	5
α-helix	375-390	16
β-strand	396	1	6
α-helix	397-398	2
β-strand	399-405	7	5
β-strand	408-414	7	5
β-strand	419-420	2	6
α-helix	421-425	5
α-helix	434-453	20
β-strand	457	1	7
β-strand	466-468	3	6
β-strand	474-476	3	6
β-strand	484	1	7
α-helix	518-521	4
α-helix	530-544	15
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	597-612	16
α-helix	618-629	12

Chain C: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	365-369	5	9
α-helix	378-390	13
β-strand	396	1	10
α-helix	397-398	2
β-strand	399-403	5	9
β-strand	410-414	5	9
β-strand	418-420	3	10
α-helix	421-426	6
α-helix	434-453	20
β-strand	457	1	11
β-strand	466-469	4	10
β-strand	474-476	3	10
β-strand	484	1	11
α-helix	518-521	4
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	597-612	16
α-helix	618-629	12

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	357	1	13
β-strand	364	1	13
β-strand	365-368	4	14
α-helix	377-388	12
β-strand	396	1	15
β-strand	399-403	5	14
β-strand	410-414	5	14
β-strand	418-420	3	15
α-helix	421-425	5
α-helix	434-452	19
β-strand	457	1	16
β-strand	466-469	4	15
β-strand	474-476	3	15
β-strand	484	1	16
α-helix	518-521	4
α-helix	530-544	15
β-strand	555-556	2	17
β-strand	560-561	2	17
α-helix	563-569	7
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-610	14
α-helix	618-629	12

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

>7ATU_1 LIM domain kinase 1 (chains A, B, C, D)
SMPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKV
MRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASG
MAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRY
TVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFL
DRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRG
FWETYRRGES

Ligands and cofactors

ID	Name	Formula	Copies
RXN	(S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin…	C24 H22 Cl N5 O4	4

Primary citation

The LIMK1 Kinase Domain Bound To LIJTF500025. Mathea, S., Chatterjee, D., Preuss, F. 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
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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