Structure of PDB 6vfw Chain C

Receptor sequence

>6vfwC (length=429) Species: 9606 (Homo sapiens)

SQLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLN
LETGVLYVNEKIDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDIND
NPPSFPEPDLTVEISESATPGTRFPLESAFDPDVGTNSLRDYEITPNSYF
SLDVQTQGDGNRFAELVLEKPLDREQQAVHRYVLTAVDGGGGGAGLPPQQ
QRTGTALLTIRVLDSNDNVPAFDQPVYTVSLPENSPPGTLVIQLNATDPD
EGQNGEVVYSFSSHISPRARELFGLSPRTGRLEVSGELDYEESPVYQVYV
QAKDLGPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVVA
LFSVTDRDSEENGQVQCELLGDVPFRLKSSFKNYYTIVTEAPLDREAGDS
YTLTVVARDRGEPALSTSKSIQVQVSDHH

3D structure

• PDB: 6vfw Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins.
• Chain: C
• 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	C	E9 E10 D63 E65 D100	E9 E10 D63 E65 D100
BS02	CA	C	E9 E65 D97 I98 D100 D133	E9 E65 D97 I98 D100 D133
BS03	CA	C	N99 N101 D131 D133 N137 D188	N99 N101 D131 D133 N137 D188
BS04	CA	C	E116 D173 E175 D228	E116 D173 E175 D217
BS05	CA	C	E116 E175 D225 S226 D228 D261	E116 E175 D214 S215 D217 D250
BS06	CA	C	N227 N229 D259 D261 N265 D315	N216 N218 D248 D250 N254 D304
BS07	CA	C	E244 D300 E302 D336	E233 D289 E291 D325
BS08	CA	C	E244 E302 D333 A334 D336 D369	E233 E291 D322 A323 D325 D358
BS09	CA	C	N335 N337 D367 D369 N373 D420	N324 N326 D356 D358 N362 D409
BS10	MAN	C	Q212 T214	Q201 T203
BS11	MAN	C	T214 T216	T203 T205

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)