Structure of PDB 6vfw Chain B

Receptor sequence

>6vfwB (length=423) Species: 9606 (Homo sapiens)

QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNL
ETGVLYVNEKIDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDN
PPSFPEPDLTVEISESATPGTRFPLESAFDPDVGTNSLRDYEITPNSYFS
LDVQTQGDGNRFAELVLEKPLDREQQAVHRYVLTAVDGGGGPPQQQRTGT
ALLTIRVLDSNDNVPAFDQPVYTVSLPENSPPGTLVIQLNATDPDEGQNG
EVVYSFSSHISPRARELFGLSPRTGRLEVSGELDYEESPVYQVYVQAKDL
GPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVVALFSVT
DRDSEENGQVQCELLGDVPFRLKSSFKNYYTIVTEAPLDREAGDSYTLTV
VARDRGEPALSTSKSIQVQVSDH

3D structure

• PDB: 6vfw Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins.
• Chain: B
• Resolution: 3.6 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	E9 E10 D63 E65 D100	E8 E9 D62 E64 D99
BS02	CA	B	E9 E65 D97 I98 D100 D133	E8 E64 D96 I97 D99 D132
BS03	CA	B	N99 N101 D131 D133 N137 D188	N98 N100 D130 D132 N136 D187
BS04	CA	B	E116 D173 E175 D228	E115 D172 E174 D212
BS05	CA	B	E116 E175 D225 S226 D228 D261	E115 E174 D209 S210 D212 D245
BS06	CA	B	N227 N229 D259 D261 N265 D315	N211 N213 D243 D245 N249 D299
BS07	CA	B	E244 D300 E302 D336	E228 D284 E286 D320
BS08	CA	B	E244 E302 D333 A334 D336 D369	E228 E286 D317 A318 D320 D353
BS09	CA	B	N335 N337 D367 D369 N373 D420	N319 N321 D351 D353 N357 D404
BS10	MAN	B	Q212 T214	Q196 T198
BS11	MAN	B	T214 T216	T198 T200

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:6vfw, PDBe:6vfw, PDBj:6vfw
• PDBsum: 6vfw
• PubMed: 32101743
• UniProt: Q9P2E7|PCD10_HUMAN Protocadherin-10 (Gene Name=PCDH10)