This code will work
import panel as pn
pn.config.js_files["ngl"]="https://cdn.jsdelivr.net/gh/arose/ngl@v2.0.0-dev.33/dist/ngl.js"
pn.extension()
html = """<div id="viewport" style="width:100%; height:100%;"></div>
<script>
stage = new ngl.Stage("viewport");
stage.loadFile("rcsb://1NKT.mmtf", {defaultRepresentation: true});
</script>"""
ngl_pane = pn.pane.HTML(html, height=500, width=500)
ngl_pane
