Structure of PDB 6vft Chain B

Receptor sequence

>6vftB (length=414) Species: 9606 (Homo sapiens)

LKNLNYSVPEEQGAGTVIGNIGRDARLQPSYRVLENSAPHLLDVDADSGL
LYTKQRIDRESLCRHNAKCQLSLEVFANDKEICMIKVEIQDINDNAPSFS
SDQIEMDISENAAPGTRFPLTSAHDPDAGENGLRTYLLTRDDHGLFGLDV
KSRGDGTKFPELVIQKALDREQQNHHTLVLTALDGGEPPRSATVQINVKV
IDSNDNSPVFEAPSYLVELPENAPLGTVVIDLNATDADEGPNGEVLYSFS
SYVPDRVRELFSIDPKTGLIRVKGNLDYEENGMLEIDVQARDLGPNPIPA
HCKVTVKLIDRNDNAPSIGFVSVRQGALSEAAPPGTVIALVRVTDRDSGK
NGQLQCRVLGGPFKLEENYDNFYTVVTDRPLDRETQDEYNVTIVARDGGS
PPLNSTKSFAIKIL

3D structure

• PDB: 6vft Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins.
• Chain: B
• Resolution: 3.71 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	CA	B	E10 E11 D74 E76 D110	E10 E11 D58 E60 D94
BS02	CA	B	E10 E76 D107 I108 D110 D143	E10 E60 D91 I92 D94 D127
BS03	CA	B	N109 N111 D141 D143 N147 D200	N93 N95 D125 D127 N131 D184
BS04	CA	B	N220 N222 D252 D254 N258 D308	N204 N206 D236 D238 N242 D292
BS05	CA	B	E126 E187 D218 S219 D221 D254	E110 E171 D202 S203 D205 D238
BS06	CA	B	E126 D185 E187 D221	E110 D169 E171 D205
BS07	CA	B	E237 D293 E295 D329	E221 D277 E279 D313
BS08	CA	B	N328 N330 D361 D363 N367 D429	N312 N314 D345 D347 N351 D397
BS09	CA	B	E237 E295 D326 R327 D329 D363	E221 E279 D310 R311 D313 D347
BS10	MAN	B	D118 T209 Q211	D102 T193 Q195
BS11	CA	B	D247 L248 N249 T283	D231 L232 N233 T267

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding

Biological Process

• GO:0007155 cell adhesion
• GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:6vft, PDBe:6vft, PDBj:6vft
• PDBsum: 6vft
• PubMed: 32101743
• UniProt: O14917|PCD17_HUMAN Protocadherin-17 (Gene Name=PCDH17)