Structure of PDB 7w9p Chain A

Receptor sequence

>7w9pA (length=1413) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSALRTFRVL
RALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMG
NLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFST
DSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQ
TLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYKEQNQANIEEAKQK
ELEFQQMLDPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPM
TEEFKNVLAIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTL
SLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGN
LTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFL
IVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLL
SSFSSDNLTAIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFGKIW
WNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKKTIKIILEY
ADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTL
GYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVC
LIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQ
NVRWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYE
YSLYMYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQ
KKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDISIMVLICLN
MVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGW
NIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAK
GIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDM
FNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEG
DCGNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVATEESTEPLSEDD
FEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDL
PMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSYE
PITTTLKRKQEDV

3D structure

• PDB: 7w9p High-resolution structures of human Na v 1.7 reveal gating modulation through alpha-pi helical transition of S6 IV.
• Chain: A
• Resolution: 2.9 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	9SL	A	Y362 E364 E927 K1406 G1407 W1408 T1409 G1699 D1701	Y343 E345 E609 K928 G929 W930 T931 G1221 D1223
BS02	P5S	A	W1179 R1182 G1249 Y1250	W701 R704 G771 Y772
BS03	Y01	A	K847 P850 L1326 I1330	K529 P532 L848 I852
BS04	Y01	A	N209 A212 V218 L219 L222 M950	N190 A193 V199 L200 L203 M632
BS05	LPE	A	F1738 S1742	F1260 S1264
BS06	1PW	A	Q360 F1452 T1696 S1697 I1744 I1745 F1748	Q341 F974 T1218 S1219 I1266 I1267 F1270
BS07	LPE	A	L1298 L1301 L1653 I1657 F1661 F1738	L820 L823 L1175 I1179 F1183 F1260
BS08	LPE	A	A1257 W1258 N1312	A779 W780 N834
BS09	P5S	A	S1490 W1578 V1624 R1631 L1634 F1635	S1012 W1100 V1146 R1153 L1156 F1157
BS10	LPE	A	F387 Y1481 F1645	F368 Y1003 F1167
BS11	LPE	A	Y1481 M1485	Y1003 M1007
BS12	LPE	A	D320 K376 T377 M379 M1655 F1692	D301 K357 T358 M360 M1177 F1214
BS13	LPE	A	Y1215 R1218 K1219 T1683 F1684	Y737 R740 K741 T1205 F1206
BS14	LPE	A	F1211 K1219 M1307 F1684	F733 K741 M829 F1206
BS15	LPE	A	W1179 Y1250	W701 Y772
BS16	P5S	A	L1566 R1570	L1088 R1092
BS17	Y01	A	L759 H765	L441 H447

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:7w9p, PDBe:7w9p, PDBj:7w9p
• PDBsum: 7w9p
• PubMed: 35476982
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)