5NXD Chain A
LIM domain kinase 2 (LIMK2)
Inactive — 2.4%DFG-outαC-outType3 · 9D8
Resolution
1.9 Å
R-value
0.197
Predicted activity confidence2.4%
Structure info
Alternate conformationA
Missing atoms5
Missing residues0
Salt bridge (KinCore)Saltbr-out
Sequence info
PDB sequence
DLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEYIEGGTLKDFLRSMDPFPWQQKVRFAKGIASGMAYLHSMCIIHRDLNSHNCLIKLDKTVVVADFGLSRLIVPYWMAPEMLNGKSYDETVDIFSFGIVLCEIIGQVYADPDCLPRTLDFGLNVKLFWEKFVPTDCPPAFFPLAAICCRLEPESRPAFSKLEDSFEALSLYLGELGIPLPAELEELDHTVSMQYGL
UniProt reference sequence
LIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEYIEGGTLKDFLRSMDPFPWQQKVRFAKGIASGMAYLHSMCIIHRDLNSHNCLIKLDKTVVVADFGLSRLIVEERKRAPMEKATTKKRTLRKNDRKKRYTVVGNPYWMAPEMLNGKSYDETVDIFSFGIVLCEIIGQVYADPDCLPRTLDFGLNVKLFWEKFVPTDCPPAFFPLAAICCRLEPESRPAFSKLEDSFEA
Aligned reference sequence
LIHG----------------EVLGKGF----------------FGQAIKVTH--KA------------------------------------TGKVMVMKELI--RCDEET----------------------------QKTFLTEVKVMRSL--------------------------DHPNVLKFIGVLYKDK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KLNLLTEYIEG--------------GTLKDFLRS--MD-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFPWQQKVRFAKGIASGMAYLHSM---------------------------------------------CIIHRDL-----NSHNCLIKL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DKTVVVADFGLSRLIVEERKR--APMEKATTKKRTLRKNDRKKR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YTVVGNPYWMAPEMLNG--------------------------------KSYD-ETVDIFSFGIVLCEIIGQ-------------------------VYADPDCLPRTL------------------------------------DFGLNVKLFWEKF--VPTDCP---------------------------------------------------------------------------------------------------------PAFFPLAAICCRLEPESRPA--------------FSKLEDSFEA
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
LIHG----------------EVLGKGF----------------FGQAIKVTH--KA------------------------------------TGKVMVMKELI--RCDEET----------------------------QKTFLTEVKVMRSL--------------------------DHPNVLKFIGVLYKDK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KLNLLTEYIEG--------------GTLKDFLRS--MD-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFPWQQKVRFAKGIASGMAYLHSM---------------------------------------------CIIHRDL-----NSHNCLIKL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DKTVVVADFGLSRLIV-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYWMAPEMLNG--------------------------------KSYD-ETVDIFSFGIVLCEIIGQ-------------------------VYADPDCLPRTL------------------------------------DFGLNVKLFWEKF--VPTDCP---------------------------------------------------------------------------------------------------------PAFFPLAAICCRLEPESRPA--------------FSKLEDSFEA
Activation segment
DFGLSRLIV-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYWMAPE
Binding pocket
EVLGKGFFGQAIKMVMKELTFLTEVKVMRSLDPNVLKFIGVNLLTEYIEGGTLKDFLRSYLHSMCIIHRDLNSHNCLIVADFGLS
Ligand info
Orthosteric ligand
9D8
Allosteric ligand
None
Ligand typeType3
Consensus conformation
DFG conformationout
αC-helix conformationout
Predicted activityinactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 5NXD, Chain A