5LVP Chain B
3-phosphoinositide-dependent protein kinase 1 (PDPK1)
Active — 79.6%DFG-inαC-inATPlike · ATP
Resolution
2.5 Å
R-value
0.176
Predicted activity confidence79.6%
Structure info
Alternate conformation—
Missing atoms0
Missing residues0
Salt bridge (KinCore)Saltbr-in
Sequence info
PDB sequence
PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
UniProt reference sequence
FKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFF
Aligned reference sequence
FKFG----------------KILGEGS----------------FSTVVLARE--LA------------------------------------TSREYAIKILE--KRHIIKENK-------------------------VPYVTRERDVMSRL--------------------------DHPFFVKLYFTFQDDE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KLYFGLSYAKN--------------GELLKYIRK--IG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SFDETCTRFYTAEIVSALEYLHGK---------------------------------------------GIIHRDL-----KPENILLNE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DMHIQITDFGTAKVLSPESKQ--ARA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NSFVGTAQYVSPELLTE--------------------------------KSAC-KSSDLWALGCIIYQLVAG-----------------LPPFRA--------------------------------------------------GNEYLIFQKIIKL--EYDFPEKFF------------------------------------------------------------------------------------------------------PKARDLVEKLLVLDATKRLG--CEEMEG------YGPLKAHPFF
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
FKFG----------------KILGEGS----------------FSTVVLARE--LA------------------------------------TSREYAIKILE--KRHIIKENK-------------------------VPYVTRERDVMSRL--------------------------DHPFFVKLYFTFQDDE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KLYFGLSYAKN--------------GELLKYIRK--IG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SFDETCTRFYTAEIVSALEYLHGK---------------------------------------------GIIHRDL-----KPENILLNE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DMHIQITDFGTAKVL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SFVGTAQYVSPELLTE--------------------------------KSAC-KSSDLWALGCIIYQLVAG-----------------LPPFRA--------------------------------------------------GNEGLIFAKIIKL--EYDFPEKFF------------------------------------------------------------------------------------------------------PKARDLVEKLLVLDATKRLG--CEEMEG------YGPLKAHPFF
Activation segment
DFGTAKVL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SFVGTAQYVSPE
Binding pocket
KILGEGSFSTVVLYAIKILYVTRERDVMSRLDPFFVKLYFTYFGLSYAKNGELLKYIRKYLHGKGIIHRDLKPENILLITDFGTA
Ligand info
Orthosteric ligand
ATP
Allosteric ligand
None
Ligand typeATPlike
Consensus conformation
DFG conformationin
αC-helix conformationin
Predicted activityactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 5LVP, Chain B