Structure of PDB 8fhd Chain A

Receptor sequence

>8fhdA (length=1294) Species: 9606 (Homo sapiens)

PDSFKPFTPESLANIERRIAESKLKPKPNSDLEAGKSLPFIYGDIPQGLV
AVPLEDFDPYYLTQKTFVVLNRGKTLFRFSATPALYILSPFNLIRRIAIK
ILIHSVFSMIIMCTILTNCVFMTFSNPPDWSKNVEYTFTGIYTFESLVKI
IARGFCIDGFTFLRDPWNWLDFSVIMMAYITEFVNLGNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
RNKCVVWPINFNESYLENGTKGFDWEEYINNKTNFYTVPGMLEPLLCGNS
SDAGQCPEGYQCMKAGRNPNYGYTSFDTFSWAFLALFRLMTQDYWENLYQ
LTLRAAGKTYMIFFVLVIFVGSFYLVNLILAVVAMAYEEQNQATLEEAEQ
KEAEFKAMLEQLKKQQEPYWIKLKEIVNLIVMDPFVDLAITICIVLNTLF
MAMEHHPMTPQFEHVLAVGNLVFTGIFTAEMFLKLIAMDPYYYFQEGWNI
FDGFIVSLSLMELSLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIG
NSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINQDCELPRWHM
HDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVFMMVMVIGNLVVL
NLFLALLLSSFSADNLAATDDDGEMNNLQISVIRIKKGCQVNIEEGLGKS
WWILRKTCFLIVEHNWFETFIIFMILLSSGALAFEDIYIEQRKTIRTILE
YADKVFTYIFILEMLLKWTAYGFVKFFTNAWCWLDFLIVAVSLVSLIANA
LGYSELGAIKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMNVLLV
CLIFWLIFSIMGVNLFAGKYHYCFNETSEIRFEIEDVNNKTECEKLMEGN
NTEIRWKNVKINFDNVGAGYLALLQVATFKGWMDIMYAAVDSRKPDEQPK
YEDNIYMYIYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTE
EQKKYYNAMKKLGSKKPQKPIPRPLNKIQGIVFDFVTQQAFDIVIMMLIC
LNMVTMMVETDTQSKQMENILYWINLVFVIFFTCECVLKMFALRHYYFTI
GWNIFDFVVVILSIVGMFLADIIEKYFVSPTLFRVIRLARIGRILRLIKG
AKGIRTLLFALMMSLPALFNIGLLLFLVMFIFSIFGMSNFAYVKHEAGID
DMFNFETFGNSMICLFQITTSAGWDGLLLPILNRPPDCSLDKEHPGSGFK
GDCGNPSVGIFFFVSYIIISFLIVVNMYIAIILENFSVATEESA

3D structure

• PDB: 8fhd Cryo-EM structure of human voltage-gated sodium channel Na v 1.6.
• Chain: A
• Resolution: 3.1 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	BMA	A	F300 W302	F273 W275
BS02	Y01	A	N1262 W1266	N779 W783
BS03	CLR	A	S857 W858	S538 W539
BS04	LPE	A	T778 F781	T459 F462
BS05	LPE	A	F1665 F1668 F1744	F1182 F1185 F1261
BS06	LPE	A	W1264 L1298	W781 L815
BS07	P5S	A	G1496 W1585 R1638 M1645	G1013 W1102 R1155 M1162
BS08	LPE	A	K385 M388 M1662	K358 M361 M1179
BS09	LPE	A	F1217 F1659 F1663	F734 F1176 F1180
BS10	Y01	A	H774 V1399	H455 V916
BS11	P5S	A	W1185 R1188 K1189 F1192 F1256 K1258	W702 R705 K706 F709 F773 K775
BS12	9Z9	A	L407 A411 F972 I1460 I1464 I1765 L1766 F1769	L380 A384 F653 I977 I981 I1282 L1283 F1286
BS13	P3X	A	F930 C934 N965 I1327 F1412 F1453 T1455	F611 C615 N646 I844 F929 F970 T972

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005248 voltage-gated sodium channel activity
• GO:0005261 monoatomic cation channel activity
• GO:0005272 sodium channel activity
• GO:0005515 protein binding
• GO:0031402 sodium ion binding

Biological Process

• GO:0001508 action potential
• GO:0006811 monoatomic ion transport
• GO:0006814 sodium ion transport
• GO:0007422 peripheral nervous system development
• GO:0019228 neuronal action potential
• GO:0021554 optic nerve development
• GO:0034220 monoatomic ion transmembrane transport
• GO:0035725 sodium ion transmembrane transport
• GO:0042552 myelination
• GO:0055085 transmembrane transport
• GO:0086002 cardiac muscle cell action potential involved in contraction

Cellular Component

• GO:0001518 voltage-gated sodium channel complex
• GO:0002102 podosome
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0030018 Z disc
• GO:0030054 cell junction
• GO:0030424 axon
• GO:0031410 cytoplasmic vesicle
• GO:0033268 node of Ranvier
• GO:0034702 monoatomic ion channel complex
• GO:0042995 cell projection
• GO:0043194 axon initial segment
• GO:0048787 presynaptic active zone membrane
• GO:0070161 anchoring junction
• GO:0098688 parallel fiber to Purkinje cell synapse
• GO:0098839 postsynaptic density membrane
• GO:0098978 glutamatergic synapse

External links

• PDB: RCSB:8fhd, PDBe:8fhd, PDBj:8fhd
• PDBsum: 8fhd
• PubMed: 36696443
• UniProt: Q9UQD0|SCN8A_HUMAN Sodium channel protein type 8 subunit alpha (Gene Name=SCN8A)