EDIT2: Another slow query example (on another database), also very simple:

# Time: 161230 12:13:39
# User@Host: ***[***] @ *** [***]
# Query_time: 4.780936  Lock_time: 0.000069 Rows_sent: 0  Rows_examined: 1
use ***;
SET timestamp=1483089219;
update ShoppingCart set cartStatus='ACQUIRED' where shoppingCartId=23423;

EDIT: MySQL Server has very good characteristics and normally queries run fast. It's a production server under high load.