Structure of PDB 8s9b Chain A

Receptor sequence

>8s9bA (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: 8s9b Structural mapping of Na v 1.7 antagonists.
• 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	LQO	A	Q360 K1406 T1696 S1697 I1744 V1751	Q339 K911 T1201 S1202 I1249 V1256
BS02	LQO	A	A402 E406 L967 L1760	A381 E385 L632 L1265
BS03	P5S	A	W1179 R1182 I1246 Y1250	W684 R687 I751 Y755
BS04	Y01	A	A1257 W1260	A762 W765
BS05	Y01	A	T758 L759 S848 W849 I1330	T428 L429 S513 W514 I835
BS06	Y01	A	V833 F837 M1338 Y1432 M1433 I1435	V498 F502 M843 Y937 M938 I940
BS07	LPE	A	I1737 S1742 I1745	I1242 S1247 I1250
BS08	LPE	A	A1257 W1258 I1315	A762 W763 I820
BS09	P5S	A	F254 L1488 G1577 W1578 F1581 L1634	F233 L993 G1082 W1083 F1086 L1139
BS10	LPE	A	Q1478 Y1481 F1645	Q983 Y986 F1150
BS11	LPE	A	D320 K376 T377 M1655	D299 K355 T356 M1160
BS12	LPE	A	A1210 F1211 M1307 F1684	A715 F716 M812 F1189
BS13	LPE	A	S257 M1533	S236 M1038
BS14	Y01	A	A762 H765 P767	A432 H435 P437

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:8s9b, PDBe:8s9b, PDBj:8s9b
• PDBsum: 8s9b
• PubMed: 37270609
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)