Structure of PDB 5vdh Chain C

Receptor sequence

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

MSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMD
YRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGAN
FHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLE
SFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKF
TCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGI
TTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFV
SRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY

3D structure

• PDB: 5vdh Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.
• Chain: C
• Resolution: 2.85 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	C	P10 Y78 L83 D84 L85	P3 Y71 L76 D77 L78	BindingDB: EC50=50nM,Kd=11nM
BS02	GLY	C	F63 R65 S129	F56 R58 S122
BS03	IVM	C	I225 Q226 I229 P230 L233	I218 Q219 I222 P223 L226
BS04	7C6	C	R27 I28 R29 F32 G160 Y161	R20 I21 R22 F25 G153 Y154	BindingDB: EC50=50nM,Kd=11nM
BS05	GLY	C	F159 Y202 T204	F152 Y195 T197
BS06	IVM	C	T264 S267 S268 A288 L291	T257 S260 S261 A281 L284
BS07	ZN	C	D194 H215	D187 H208

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