Structure of PDB 8i5b Chain A

Receptor sequence

>8i5bA (length=1272) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNVSALRTFRVLRAL
KTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLK
HKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDSG
QCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLR
AAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYWI
KFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNL
VFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLRS
FRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQ
LFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCM
EVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDAN
NLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFES
FIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKWI
AYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALR
PLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGK
FYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGY
LSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSF
FTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKP
IPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEV
LYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLA
DLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALFN
IGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITT
SAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIII
SFLVVVNMYIAVILENFSVATE

3D structure

• PDB: 8i5b Structural mapping of Na v 1.7 antagonists.
• Chain: A
• Resolution: 2.7 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	P5S	A	W1178 W1179 R1182 W1245 I1246 Y1250	W682 W683 R686 W749 I750 Y754
BS02	Y01	A	Y1250 K1251 T1255	Y754 K755 T759
BS03	Y01	A	V755 T758 S848 W849 I1330	V424 T427 S512 W513 I834
BS04	Y01	A	Y1432 I1435	Y936 I939
BS05	Y01	A	A212 F216 I876 F880 M943 M950	A190 F194 I540 F544 M607 M614
BS06	Y01	A	H765 P767	H434 P436
BS07	LPE	A	S1734 I1737 F1738 S1742 I1745	S1238 I1241 F1242 S1246 I1249
BS08	LPE	A	A1257 W1258 L1295 V1311 N1312	A761 W762 L799 V815 N816
BS09	LPE	A	K1480 Y1481	K984 Y985
BS10	LPE	A	D320 K376 M379 M1655	D298 K354 M357 M1159
BS11	LPE	A	L1203 F1211	L707 F715
BS12	LPE	A	S257 G1626	S235 G1130
BS13	OJ0	A	L968 I1457 D1458 L1760	L632 I961 D962 L1264

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:8i5b, PDBe:8i5b, PDBj:8i5b
• PDBsum: 8i5b
• PubMed: 37270609
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)