Structure of PDB 6vfr Chain A

Receptor sequence

>6vfrA (length=428) Species: 9606 (Homo sapiens)

KNLKYRIYEEQRVGSVIARLSEDVADVLLKLPNPSTVRFRAMQRGNSPLL
VVNEDNGEISIGATIDREQLCQKNLNCSIEFDVITLPTEHLQLFHIEVEV
LDINDNSPQFSRSLIPIEISESAAVGTRIPLDSAFDPDVGENSLHTYSLS
ANDFFNIEVRTRTDGAKYAELIVVRELDRELKSSYELQLTASDMGVPQRS
GSSILKISISDSNDNSPAFEQQSYIIQLLENSPVGTLLLDLNATDPDEGA
NGKIVYSFSSHVSPKIMETFKIDSERGHLTLFKQVDYEITKSYEIDVQAQ
DLGPNSIPAHCKIIIKVVDVNDNKPEININLMSPGKEEISYIFEGDPIDT
FVALVRVQDKDSGLNGEIVCKLHGHGHFKLQKTYENNYLILTNATLDREK
RSEYSLTVIAEDRGTPSLSTVKHFTVQI

3D structure

• PDB: 6vfr Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins.
• Chain: A
• Resolution: 2.79 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	A	N104 N106 D136 D138 N142 D193	N104 N106 D136 D138 N142 D193
BS02	CA	A	E9 E68 D102 I103 D105 D138	E9 E68 D102 I103 D105 D138
BS03	CA	A	E9 E10 D66 E68 D105	E9 E10 D66 E68 D105
BS04	CA	A	E121 E180 D211 S212 D214 D247	E121 E180 D211 S212 D214 D247
BS05	CA	A	E121 D178 E180 D214	E121 D178 E180 D214
BS06	CA	A	N213 N215 D245 D247 N251 D301	N213 N215 D245 D247 N251 D301
BS07	CA	A	E230 E288 D319 V320 D322 D361	E230 E288 D319 V320 D322 D361
BS08	CA	A	E230 D286 E288 D322	E230 D286 E288 D322
BS09	CA	A	N321 N323 D359 D361 N365 D412	N321 N323 D359 D361 N365 D412

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:6vfr, PDBe:6vfr, PDBj:6vfr
• PDBsum: 6vfr
• PubMed: 32101743
• UniProt: Q9HCL0|PCD18_HUMAN Protocadherin-18 (Gene Name=PCDH18)