5HVJ: LIMK1 D460N mutant

Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP. Determined by X-ray diffraction at 2.2 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,720
Mol. weight: 73.29 kDa
Ligands: ANP
Released: 4 May 2016

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

Secondary structure: helices and β-sheets

5HVJ contains 26 α-helices and 29 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	339-347	9	1
β-strand	352-358	7	1
β-strand	364-369	6	1
α-helix	375-388	14
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	513-515	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	595-596	2
α-helix	597-613	17
α-helix	619-631	13

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	333	1	5
β-strand	339-344	6	6
β-strand	352-358	7	6
β-strand	364-369	6	6
α-helix	375-388	14
β-strand	396	1	7
α-helix	397-398	2
β-strand	399-401	3	6
β-strand	402	1	5
β-strand	410-414	5	6
β-strand	420	1	7
α-helix	421-426	6
α-helix	434-453	20
β-strand	457	1	8
β-strand	466-468	3	7
β-strand	474-476	3	7
β-strand	483	1	8
α-helix	518-521	4
α-helix	530-544	15
β-strand	555	1	9
β-strand	561	1	9
α-helix	563-569	7
α-helix	576	1
α-helix	579-586	8
α-helix	595-596	2
α-helix	597-611	15
α-helix	619-632	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	A, B	protein	315	Homo sapiens	P53667 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5HVJ_1 LIM domain kinase 1 (chains A, B)
GAMGSRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLK
EVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKD
IASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDR
KKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNV
RGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQ
LDRGFWETYRRGESG

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Hamill, S., Lou, H.J., Turk, B.E. et al. Mol Cell (2016) 62:397-408. DOI 10.1016/j.molcel.2016.04.001 · 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
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

Browse structure collections

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