5M57 Chain A
Serine/threonine-protein kinase Nek2 (NEK2)
Inactive — 0.0%DFG-inαC-outType1 · 4SP
Resolution
2.3 Å
R-value
0.221
Predicted activity confidence0.0%
Structure info
Alternate conformation—
Missing atoms26
Missing residues3
Salt bridge (KinCore)Saltbr-none
Sequence info
PDB sequence
SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
UniProt reference sequence
YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLI
Aligned reference sequence
YEVL----------------YTIGTGS----------------YGRCQKIRR--KS------------------------------------DGKILVWKELD--YGSMTEAE--------------------------KQMLVSEVNLLREL--------------------------KHPNIVRYYDRIIDRT--NT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TLYIVMEYCEG--------------GDLASVITK--GTKERQ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YLDEEFVLRVMTQLTLALKECHRR--SDGGH--------------------------------------TVLHRDL-----KPANVFLDG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KQNVKLGDFGLARILNHDTSF--A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KTFVGTPYYMSPEQMNR--------------------------------MSYN-EKSDIWSLGCLLYELCAL-----------------MPPFTA--------------------------------------------------FSQKELAGKIREG--KFRRIPYRYS-----------------------------------------------------------------------------------------------------DELNEIITRMLNLKDYHRPS--------------VEEILENPLI
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
YEVL----------------YTIGTGS----------------YGRCQKIRR--KS------------------------------------DGKILVWKELD--YGSMTEAE--------------------------KQMLVSEVNLLREL--------------------------KHPNIVRYYDRIIDRT--NT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TLYIVMEYCEG--------------GDLASVITK--GTKERQ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YLDEEFVLRVMTQLTLALKECHRR--SDGGH--------------------------------------TVLHRDL-----KPANVFLDG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KQNVKLGD---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FVGTPYYMSPEQMNR--------------------------------MSYN-EKSDIWSLGCLLYELCAL-----------------MPPFTA--------------------------------------------------FSQKELAGKIREG--KFRRIPYRYS-----------------------------------------------------------------------------------------------------DELNEIITRMLNLKDYHRPS--------------VEEILENPLI
Activation segment
D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FVGTPYYMSPE
Binding pocket
YTIGTGSYGRCQKLVWKELMLVSEVNLLRELKPNIVRYYDRYIVMEYCEGGDLASVITKSDGGHTVLHRDLKPANVFLLGDF___
Ligand info
Orthosteric ligand
4SP
Allosteric ligand
None
Ligand typeType1
Consensus conformation
DFG conformationin
αC-helix conformationout
Predicted activityinactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 5M57, Chain A