5VD3 Chain A
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (PKMYT1)
Active — 99.3%DFG-inαC-inType1 · H8H
Resolution
1.8 Å
R-value
0.167
Predicted activity confidence99.3%
Structure info
Alternate conformation—
Missing atoms0
Missing residues0
Salt bridge (KinCore)Saltbr-in
Sequence info
PDB sequence
DLGTENLYFQQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLR
UniProt reference sequence
FQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVL
Aligned reference sequence
FQRL----------------SRLGHGS----------------YGEVFKVRS--KE------------------------------------DGRLYAVKRSM--SPFRGPKD--------------------------RARKLAEVGSHEKV--G-----------------------QHPCCVRLEQAWEEGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ILYLQTELCG---------------PSLQQHCEA--WGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SLPEAQVWGYLRDTLLALAHLHSQ---------------------------------------------GLVHLDV-----KPANIFLGP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RGRCKLGDFGLLVELGTAGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EVQEGDPRYMAPELLQ---------------------------------GSYG-TAADVFSLGLTILEVACN-------------------------MEL---------------------------------------------PHGGEGWQQLRQG--YLPPEFTAGLS----------------------------------------------------------------------------------------------------SELRSVLVMMLEPDPKLRAT--------------AEALLALPVL
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
FQRL----------------SRLGHGS----------------YGEVFKVRS--KE------------------------------------DGRLYAVKRSM--SPFRGPKD--------------------------RARKLAEVGSHEKV--G-----------------------QHPCCVRLEQAWEEGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ILYLQTELCG---------------PSLQQHCEA--WGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SLPEAQVWGYLRDTLLALAHLHSQ---------------------------------------------GLVHLDV-----KPANIFLGP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RGRCKLGDFGLLVELGTAGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EVQEGDPRYMAPELLQ---------------------------------GSYG-TAADVFSLGLTILEVACN-------------------------MEL---------------------------------------------PHGGEGWQQLRQG--YLPPEFTAGLS----------------------------------------------------------------------------------------------------SELRSVLVMMLEPDPKLRAT--------------AEALLALPVL
Activation segment
DFGLLVELGTAGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EVQEGDPRYMAPE
Binding pocket
SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC_GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL
Ligand info
Orthosteric ligand
H8H
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 5VD3, Chain A