3S95 | pdb_00003s95

Crystal structure of the human LIMK1 kinase domain in complex with staurosporine

• PDB DOI: https://doi.org/10.2210/pdb3S95/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-05-31 Released: 2011-07-06 
• Deposition Author(s): Beltrami, A., Chaikuad, A., Daga, N., Elkins, J.M., Mahajan, P., Savitsky, P., Vollmar, M., Krojer, T., Muniz, J.R.C., Fedorov, O., Allerston, C.K., Yue, W.W., Gileadi, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the human LIMK1 kinase domain in complex with staurosporine

Beltrami, A., Chaikuad, A., Daga, N., Elkins, J.M., Mahajan, P., Savitsky, P., Vollmar, M., Krojer, T., Muniz, J.R.C., Fedorov, O., Allerston, C.K., Yue, W.W., Gileadi, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.41 kDa 
• Atom Count: 5,508 
• Modeled Residue Count: 580 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 1	A, B	310	Homo sapiens	Mutation(s): 0  Gene Names: LIMK, LIMK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53667 (Homo sapiens) Explore P53667  Go to UniProtKB:  P53667
PHAROS:  P53667 GTEx:  ENSG00000106683

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	C [auth A], P [auth B]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N
TRS	O [auth A], V [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MRD	T [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	N [auth A], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STU	BindingDB:  3S95	IC50: 2.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.16	α = 90
b = 128	β = 90
c = 131.35	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-06 
Deposition Author(s): Beltrami, A., Chaikuad, A., Daga, N., Elkins, J.M., Mahajan, P., Savitsky, P., Vollmar, M., Krojer, T., Muniz, J.R.C., Fedorov, O., Allerston, C.K., Yue, W.W., Gileadi, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description