3S95

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 3S95

Classification: TRANSFERASE / ANTIBIOTIC

Total Structure Weight: 74414.98

Macromolecule Entities
Molecule Chains Length Organism Details
LIM domain kinase 1 A, B 310 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: kinase domain (residue 330-637)
Gene Name(s): LIMK1 Gene View LIMK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
STU
Query on STU

A, B STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A, B 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

B (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
STU Kd: 48 - 690 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.155
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 106.16 α = 90.00
b = 128.00 β = 90.00
c = 131.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-31
  • 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

    Type: Version format compliance