Structure of PDB 8uo8 Chain A

Receptor sequence

>8uo8A (length=574) Species: 9606 (Homo sapiens)

DEEQLAHQYETIMDECGHGRFQWILFFVLGLALMADGVEVFVVSFALPSA
EKDMCLSSSKKGMLGMIVYLGMMAGAFILGGLADKLGRKRVLSMSLAVNA
SFASLSSFVQGYGAFLFCRLISGIGIGGALPIVFAYFSEFLSREKRGEHL
SWLGIFWMTGGLYASAMAWSIIPHYGWGFSMGTNYHFHSWRVFVIVCALP
CTVSMVALKFMPESPRFLLEMGKHDEAWMILKQVHDTNMRAKGTPEKVFT
VSNIKTPFKTIFKQVWDNALYCVMGPYRMNTLILAVVWFAMAFSYYGLTV
WFPDMIRYFQDEEYKSKMKVFFGEHVYGATINFTMENQIHQHGKLVNDKF
TRMYFKHVLFEDTFFDECYFEDVTSTDTYFKNCTIESTIFYNTDLYEHKF
INCRFINSTFLEQKEGCHMDLEQDNDFLIYLVSFLGSLSVLPGNIISALL
MDRIGRLKMIGGSMLISAVCCFFLFFGNSESAMIGWQCLFCGTSIAAWNA
LDVITVELYPTNQRATAFGILNGLCKFGAILGNTIFASFVGITKVVPILL
AAASLVGGGLIALRLPETREQVLM

3D structure

• PDB: 8uo8 Structure of synaptic vesicle protein 2B with padsevonil
• Chain: A
• Resolution: 3.2 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	X3U	A	F220 W243 W397 Y404 Y405 V549 S603 I604 W607 D611 N631 C634 K635	F134 W157 W288 Y295 Y296 V440 S494 I495 W498 D502 N522 C525 K526
BS02	PS1	A	H104 G105 W109 F113	H18 G19 W23 F27
BS03	9Z9	A	T245 S256	T159 S170
BS04	9Z9	A	E234 L558	E148 L449
BS05	43Y	A	M253 I257 Y271 S275 V278	M167 I171 Y185 S189 V192
BS06	Y01	A	P551 G552 G571 G601 T602	P442 G443 G462 G492 T493

Gene Ontology

Molecular Function

• GO:0005515 protein binding

Biological Process

• GO:0006836 neurotransmitter transport
• GO:0099509 regulation of presynaptic cytosolic calcium ion concentration
• GO:2000300 regulation of synaptic vesicle exocytosis

Cellular Component

• GO:0001669 acrosomal vesicle
• GO:0005886 plasma membrane
• GO:0008021 synaptic vesicle
• GO:0016020 membrane
• GO:0030672 synaptic vesicle membrane
• GO:0031410 cytoplasmic vesicle
• GO:0045202 synapse

External links

• PDB: RCSB:8uo8, PDBe:8uo8, PDBj:8uo8
• PDBsum: 8uo8
• PubMed: 38898101
• UniProt: Q7L1I2|SV2B_HUMAN Synaptic vesicle glycoprotein 2B (Gene Name=SV2B)