6NCG Chain A
Serine/threonine-protein kinase VRK2 (VRK2)
Active — 99.6%DFG-inαC-inType1.5_Back · KJD
Resolution
2.45 Å
R-value
0.224
Predicted activity confidence99.6%
Structure info
Alternate conformation—
Missing atoms38
Missing residues4
Salt bridge (KinCore)Saltbr-none
Sequence info
PDB sequence
PFPEGKVLDDMEGNQWVLGKKIGSFGLIYLAFPTNKPKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFS
UniProt reference sequence
WVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNP
Aligned reference sequence
WVLG----------------KKIGSGG----------------FGLIYLAFP--TNKPE---------------------------------KDARHVVKVEY--QE--------------------------------NGPLFSELKFYQRV--AKKDCIKKWIERKQLDY---------LGIPLFYGSGLTEF--KGRS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YRFMVMERLG---------------IDLQKISGQ--NG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TFKKSTVLQLGIRMLDVLEYIHEN---------------------------------------------EYVHGDI-----KAANLLLGY--KN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDQVYLADYGLSYRYCPNGNH--KQYQENPR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KGHNGTIEFTSLDAHKG--------------------------------VALS-RRSDVEILGYCMLRWLCG-----------------KLPWEQ--NL----------------------------------------------KDPVAVQTAKTNL--LDELPQSVLKWAPSGSSC---------------------------------------------------------------------------------------------CEIAQFLVCAHSLAYDEKPN--------------YQALKKILNP
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
WVLG----------------KKIGS------------------FGLIYLAFP--TNKP----------------------------------KDARHVVKVEY--QE--------------------------------NGPLFSELKFYQRV--AKKDCIKKWIERKQLDY---------LGIPLFYGSGLTEF--KGRS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YRFMVMERLG---------------IDLQKIS----NG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TFKKSTVLQLGIRMLDVLEYIHEN---------------------------------------------EYVHGDI-----KAANLLLGY--KN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDQVYLADYGLSYRYCPNGNH--KQYQENPR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KGHNGTIEFTSLDAHKG--------------------------------VALS-RRSDVEILGYCMLRWLCG-----------------KLPWEQ--NL----------------------------------------------KDPVAVQTAKTNL--LDELPQSVLKWAPSGSSC---------------------------------------------------------------------------------------------CEIAQFLVCAHSLAYDEKPN--------------YQALKKILNP
Activation segment
DYGLSYRYCPNGNH--KQYQENPR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KGHNGTIEFTSLD
Binding pocket
KKIGS__FGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG_IDLQKIS__YIHENEYVHGDIKAANLLLLADYGLS
Ligand info
Orthosteric ligand
KJD
Allosteric ligand
None
Ligand typeType1.5_Back
Consensus conformation
DFG conformationin
αC-helix conformationin
Predicted activityactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 6NCG, Chain A