Structure of PDB 7xvf Chain A

Receptor sequence

>7xvfA (length=1261) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVKYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNVSALRTFRVLRAL
KTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLK
HKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDSG
QCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLR
AAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKCSPYW
IKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIRN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFGLSVLR
SFRLLRVFKLAKSWPTLNMLIKIIGNSVGAFGNLMLVLFIIVFIFAVVGM
QLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC
MEVAGQAMCLIFYMMVFFIGNLVVLNLFLALLLSSFSANNLQIAVTRIKK
GINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSG
ALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNA
WCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGM
RVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYECINTTDGS
RFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYLSLLQVATFKG
WTIIMYAAVDSVNVDKQPKYEYSLYMYIYFIFFIIFGSFFTLNLFICVII
DNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGC
IFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIIL
FTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPT
LFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFI
YAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITTSAGWDGLLAPI
LNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIA
VILENFSVATE

3D structure

• PDB: 7xvf Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7.
• Chain: A
• Resolution: 2.8 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	Y01	A	A762 H765 P767	A432 H435 P437
BS02	CLR	A	G867 F874	G532 F539
BS03	LPE	A	L759 M763 F772	L429 M433 F442
BS04	LPE	A	N1732 P1733 S1734	N1225 P1226 S1227
BS05	1PW	A	I1745 L1749	I1238 L1242
BS06	LPE	A	S1288 Y1658 F1661 N1665 F1738	S781 Y1151 F1154 N1158 F1231
BS07	LPE	A	A1257 W1258	A750 W751
BS08	LPE	A	T1475 Q1478	T968 Q971
BS09	LPE	A	D320 K376 M379 F1652	D298 K354 M357 F1145
BS10	LPE	A	T1683 G1685	T1176 G1178
BS11	LPE	A	F1211 F1652 F1656	F704 F1145 F1149
BS12	Y01	A	F1335 S1430 Y1432 M1433 I1435 Y1436 F1439	F828 S923 Y925 M926 I928 Y929 F932
BS13	Y01	A	E1428 Y1429	E921 Y922
BS14	Y01	A	W1245 Y1250 F1254	W738 Y743 F747
BS15	LPE	A	W1178 W1179 R1182	W671 W672 R675
BS16	LPE	A	W1179 R1182 W1245 Y1248 Y1250	W672 R675 W738 Y741 Y743
BS17	LPE	A	G1175 W1178	G668 W671
BS18	LPE	A	I1188 H1191 F1194	I681 H684 F687

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

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0006814 sodium ion transport
• GO:0006954 inflammatory response
• GO:0007623 circadian rhythm
• GO:0009636 response to toxic substance
• GO:0009791 post-embryonic development
• GO:0019228 neuronal action potential
• GO:0019233 sensory perception of pain
• GO:0034220 monoatomic ion transmembrane transport
• GO:0035725 sodium ion transmembrane transport
• GO:0048266 behavioral response to pain
• GO:0050965 detection of temperature stimulus involved in sensory perception of pain
• GO:0050974 detection of mechanical stimulus involved in sensory perception
• GO:0055085 transmembrane transport
• GO:0086002 cardiac muscle cell action potential involved in contraction
• GO:0098870 action potential propagation

Cellular Component

• GO:0001518 voltage-gated sodium channel complex
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0030424 axon
• GO:0033268 node of Ranvier
• GO:0034702 monoatomic ion channel complex
• GO:0042995 cell projection
• GO:0043005 neuron projection
• GO:0043679 axon terminus

External links

• PDB: RCSB:7xvf, PDBe:7xvf, PDBj:7xvf
• PDBsum: 7xvf
• PubMed: 35878056
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)