6NCG Chain B
Serine/threonine-protein kinase VRK2 (VRK2)
Active — 99.2%DFG-inαC-inType1.5_Back · KJD
Resolution
2.45 Å
R-value
0.224
Predicted activity confidence99.2%
Structure info
Alternate conformation—
Missing atoms32
Missing residues2
Salt bridge (KinCore)Saltbr-out
Sequence info
PDB sequence
PEGKVLDDMEGNQWVLGKKIGSFGLIYLAFPTNKKDARHVVKVENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFS
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--TNK-----------------------------------KDARHVVKV-----E--------------------------------NGPLFSELKFYQRV--AKKDCIKKWIERKQLDY---------LGIPLFYGSGLTEF----RS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YRFMVMERLG---------------IDLQKISGQ--NG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TFKKSTVLQLGIRMLDVLEYIHEN---------------------------------------------EYVHGDI-----KAANLLLGY--KN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDQVYLADYGLSYRYCP-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NGTIEFTSLDAHKG--------------------------------VALS-RRSDVEILGYCMLRWLCG-----------------KLPWEQ--NL----------------------------------------------KDPVAVQTAKTNL--LDELPQSVLKWAPSGSSC---------------------------------------------------------------------------------------------CEIAQFLVCAHSLAYDEKPN--------------YQALKKILNP
Activation segment
DYGLSYRYCP-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NGTIEFTSLD
Binding pocket
KKIGS__FGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG_IDLQKISGQYIHENEYVHGDIKAANLLLLADYGLS
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 B