Structure of PDB 5vdi Chain A

Receptor sequence

>5vdiA (length=338) Species: 9606 (Homo sapiens)

MSPSDFLDKLMGRTSGYDARIRPNFKGPPVQVTCNIFINSFGSIAETTMD
YRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGAN
FHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLE
SFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKF
TCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGI
TTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFV
SRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY

3D structure

• PDB: 5vdi Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.
• Chain: A
• Resolution: 3.1 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	7C6	A	I28 R29 F32 G160 Y161	I21 R22 F25 G153 Y154	BindingDB: EC50=50nM,Kd=11nM
BS02	GLY	A	F159 T204	F152 T197
BS03	IVM	A	S267 V280 A288 L291	S260 V273 A281 L284
BS04	ZN	A	D194 H215	D187 H208
BS05	7C6	A	P10 Y78 D84 L85	P3 Y71 D77 L78	BindingDB: EC50=50nM,Kd=11nM
BS06	GLY	A	F63 R65 S129	F56 R58 S122
BS07	IVM	A	I225 I229 P230	I218 I222 P223

Gene Ontology

Molecular Function

• GO:0004888 transmembrane signaling receptor activity
• GO:0005216 monoatomic ion channel activity
• GO:0005230 extracellular ligand-gated monoatomic ion channel activity
• GO:0016594 glycine binding
• GO:0022824 transmitter-gated monoatomic ion channel activity

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0034220 monoatomic ion transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:5vdi, PDBe:5vdi, PDBj:5vdi
• PDBsum: 5vdi
• PubMed: 28479061
• UniProt: O75311|GLRA3_HUMAN Glycine receptor subunit alpha-3 (Gene Name=GLRA3)