Structure of PDB 8i5g Chain A

Receptor sequence

>8i5gA (length=1273) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
KHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDS
GQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTL
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYW
IKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLR
SFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGM
QLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC
MEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDA
NNLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFE
SFIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKW
IAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRAL
RPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAG
KFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLG
YLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGS
FFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQK
PIPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTE
VLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFL
ADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALF
NIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQIT
TSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYII
ISFLVVVNMYIAVILENFSVATE

3D structure

• PDB: 8i5g 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	Y01	A	T758 W849 P850 E981 I1330	T428 W514 P515 E646 I835
BS02	9Z9	A	L398 E406 Q410 F963 L964 L968 I1457 I1759	L377 E385 Q389 F628 L629 L633 I962 I1264
BS03	T70	A	Y1548 W1549 N1551 V1552 G1592 M1593 D1597 E1600 F1609 R1613 A1615 R1616 R1619	Y1053 W1054 N1056 V1057 G1097 M1098 D1102 E1105 F1114 R1118 A1120 R1121 R1124
BS04	NA	A	D361 E927 W928 I929 E930	D340 E592 W593 I594 E595
BS05	LPE	A	P1733 S1734 I1737 F1738 S1742	P1238 S1239 I1242 F1243 S1247
BS06	LPE	A	Y1658 F1661 Y1739	Y1163 F1166 Y1244
BS07	LPE	A	A1257 W1258 N1312	A762 W763 N817
BS08	LPE	A	F387 Y1481 L1641 P1642 F1645	F366 Y986 L1146 P1147 F1150
BS09	LPE	A	D320 K376 T377	D299 K355 T356
BS10	LPE	A	G1207 A1210 F1211 M1307 F1656 F1684	G712 A715 F716 M812 F1161 F1189
BS11	LPE	A	K1187 H1191 F1194 F1197	K692 H696 F699 F702

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:8i5g, PDBe:8i5g, PDBj:8i5g
• PDBsum: 8i5g
• PubMed: 37270609
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)