2VN9 Chain A
Calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D)
Active — 99.9%DFG-inαC-inType1 · GVD
Resolution
2.3 Å
R-value
0.213
Predicted activity confidence99.9%
Structure info
Alternate conformation—
Missing atoms10
Missing residues0
Salt bridge (KinCore)Saltbr-in
Sequence info
PDB sequence
SMTDEYQLFEELGKGAFSVVRRCMKIPTGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLKGAILTTML
UniProt reference sequence
YQLFEELGKGAFSVVRRCMKIPTGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWI
Aligned reference sequence
YQLF----------------EELGKGA----------------FSVVRRCMK--IP------------------------------------TGQEYAAKIIN--TKKLSARD--------------------------HQKLEREARICRLL--------------------------KHPNIVRLHDSISEEG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FHYLVFDLVTG--------------GELFEDIVA--RE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YYSEADASHCIQQILESVNHCHLN---------------------------------------------GIVHRDL-----KPENLLLAS--KSK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAVKLADFGLAIEVQGDQQA--W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGFAGTPGYLSPEVLRK--------------------------------DPYG-KPVDMWACGVILYILLVG-----------------YPPFWD--------------------------------------------------EDQHRLYQQIKAG--AYDFPSPEWDTVT--------------------------------------------------------------------------------------------------PEAKDLINKMLTINPAKRIT--------------ASEALKHPWI
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
YQLF----------------EELGKGA----------------FSVVRRCMK--IP------------------------------------TGQEYAAKIIN--TKKLSARD--------------------------HQKLEREARICRLL--------------------------KHPNIVRLHDSISEEG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FHYLVFDLVTG--------------GELFEDIVA--RE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YYSEADASHCIQQILESVNHCHLN---------------------------------------------GIVHRDL-----KPENLLLAS--KSK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAVKLADFGLAIEVQGDQQA--W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGFAGTPGYLSPEVLRK--------------------------------DPYG-KPVDMWACGVILYILLVG-----------------YPPFWD--------------------------------------------------EDQHRLYQQIKAG--AYDFPSPEWDTVT--------------------------------------------------------------------------------------------------PEAKDLINKMLTINPAKRIT--------------ASEALKHPWI
Activation segment
DFGLAIEVQGDQQA--W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGFAGTPGYLSPE
Binding pocket
EELGKGAFSVVRRYAAKIIKLEREARICRLLKPNIVRLHDSYLVFDLVTGGELFEDIVAHCHLNGIVHRDLKPENLLLLADFGLA
Ligand info
Orthosteric ligand
GVD
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 2VN9, Chain A