3OP5 Chain A
Serine/threonine-protein kinase VRK1 (VRK1)
Active — 99.9%DFG-inαC-inType1 · REB
Resolution
2.4 Å
R-value
0.179
Predicted activity confidence99.9%
Structure info
Alternate conformationA
Missing atoms6
Missing residues1
Salt bridge (KinCore)Saltbr-out
Sequence info
PDB sequence
EQFAVGEIITDMAAAAWKVGLPIGQGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL
UniProt reference sequence
WKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEKNKPGEIAKYMETVKLLDYTEKPLYENLRDILLQ
Aligned reference sequence
WKVG----------------LPIGQGG----------------FGCIYLADM--NSSESVG-------------------------------SDAPCVVKVEP--SD--------------------------------NGPLFTELKFYQRA--AKPEQIQKWIRTRKLKY---------LGVPKYWGSGLHDK--NGKS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YRFMIMDRFG---------------SDLQKIYEA--NAK------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RFSRKTVLQLSLRILDILEYIHEH---------------------------------------------EYVHGDI-----KASNLLLNY--KN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDQVYLVDYGLAYRYCPEGVH--KEYKEDPK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RCHDGTIEFTSIDAHNG--------------------------------VAPS-RRGDLEILGYCMIQWLTG-----------------HLPWED--NL----------------------------------------------KDPKYVRDSKIRY--RENIASLMDKCFPEKNKP---------------------------------------------------------------------------------------------GEIAKYMETVKLLDYTEKPL--------------YENLRDILLQ
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
WKVG----------------LPIGQ-G----------------FGCIYLADM--NSSESVG-------------------------------SDAPCVVKVEP--SD--------------------------------NGPLFTELKFYQRA--AKPEQIQKWIRTRKLKY---------LGVPKYWGSGLHDK--NGKS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YRFMIMDRFG---------------SDLQKIYEA--NAK------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RFSRKTVLQLSLRILDILEYIHEH---------------------------------------------EYVHGDI-----KASNLLLNY--KN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDQVYLVDYGLAYRYCPEGVH--KAYAADPK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RCHDGTIEFTSIDAHNG--------------------------------VAPS-RRGDLEILGYCMIQWLTG-----------------HLPWED--NL----------------------------------------------KDPKYVRDSKIRY--RENIASLMDKCFPAANAP---------------------------------------------------------------------------------------------GEIAKYMETVKLLDYTEKPL--------------YENLRDILLQ
Activation segment
DYGLAYRYCPEGVH--KAYAADPK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RCHDGTIEFTSID
Binding pocket
LPIGQG_FGCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG_SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA
Ligand info
Orthosteric ligand
REB
Allosteric ligand
None
Ligand typeType1
Consensus conformation
DFG conformationin
αC-helix conformationin
Predicted activityactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 3OP5, Chain A