Structure of PDB 8xmm Chain A

Receptor sequence

>8xmmA (length=1145) Species: 9606 (Homo sapiens)

PLRRISIKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIY
TFESLVKILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSAL
RTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIG
LQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDAL
LCGFSTDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYW
ENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANI
EEAKCSPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEE
FKNVLAIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLV
ELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGAFGNLML
VLFIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVF
RVLCGEWIETMWDCMEVAGQAMCLIFYMMVFFIGNLVVLNLFLALLLSSF
SGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKKTIK
IILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTL
VANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMN
VLLVCLIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFAL
MNVSQNVRWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDK
QPKYEYSLYMYIYFIFFIIFGSFFTLNLFICVIIDNFNQQKKKLGGQDIF
MTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDISIMV
LICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYY
FTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRL
VKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKED
GINDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPG
SSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVATE

3D structure

• PDB: 8xmm Dissection of the structure-function relationship of Na v channels.
• Chain: A
• Resolution: 2.89 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	CLR	A	A762 H765 V1392	A341 H344 V769
BS02	LPE	A	N1732 S1734 S1742	N1109 S1111 S1119
BS03	1PW	A	I1321 M1322 T1404 F1452 F1748	I698 M699 T781 F829 F1125
BS04	LPE	A	S1288 Y1658 F1661 F1738	S665 Y1035 F1038 F1115
BS05	LPE	A	W1258 N1312	W635 N689
BS06	LPE	A	D320 M379 Y1215	D207 M266 Y592
BS07	LPE	A	S1206 F1211 L1653 F1656	S583 F588 L1030 F1033
BS08	LPE	A	W1178 R1182 Y1186 I1246 G1249 Y1250	W555 R559 Y563 I623 G626 Y627
BS09	P5S	A	L1566 I1567 R1570 H1571	L943 I944 R947 H948

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:8xmm, PDBe:8xmm, PDBj:8xmm
• PDBsum: 8xmm
• PubMed: 38381792
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)