Structure of PDB 6pgw Chain A

Receptor sequence

>6pgwA (length=427) Species: 7955 (Danio rerio)

VFDEPVYTVNVLENSPINTLVIDLNATDPDEGTNGEVVYSFINFVSNLTK
QMFKIDPKTGVITVNGVLDHEELHIHEIDVQAKDLGPNSIPAHCKVIVNV
IDINDNAPEIKLLSENSEMVEVSENAPLGYVIALVRVSDNDSGANGKVQC
RLQGNVPFRLNEFESFSTLLVDGRLDREQRDMYNLTILAEDSGYPPLRSS
KSFAVKVTDENDNPPYFTKPHYQAMVLENNVPGAFLLAVSARDPDLGMNG
TVSYEIIKSEVRGMSVESYVTVNSNGEIYGVRAFNHEDTRTFEFKVSAKD
GGDPPLTSNATVRIVVLDVNDNTPVMTTPPLVNGTAEVSIPKNAGVGYLV
TQIKADDYDEGENGRLTYSISEGDMAYFEIDQINGEVRTTKTFGENAKPS
YQITVVAHDHGQTSLSASAYIVIYLSP

3D structure

• PDB: 6pgw A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and potential protein interaction sites.
• Chain: A
• Resolution: 3.0 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	E226 D282 E284 D318	E13 D69 E71 D105
BS02	CA	A	E226 E284 D315 I316 D318 D354	E13 E71 D102 I103 D105 D141
BS03	CA	A	N317 N319 D352 D354 N358 D404	N104 N106 D139 D141 N145 D191
BS04	CA	A	E337 D389 E391 D425	E124 D176 E178 D212
BS05	CA	A	E337 E391 D422 E423 D425 D458	E124 E178 D209 E210 D212 D245
BS06	CA	A	N424 N426 D456 D458 N462 D513	N211 N213 D243 D245 N249 D300
BS07	CA	A	E441 N498 E500 D534	E228 N285 E287 D321
BS08	CA	A	E441 E500 D531 V532 D534 D572	E228 E287 D318 V319 D321 D359
BS09	CA	A	N533 N535 D570 D572 N576 D622	N320 N322 D357 D359 N363 D409

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:6pgw, PDBe:6pgw, PDBj:6pgw
• PDBsum: 6pgw
• PubMed: 34520737
• UniProt: F8W3X3|PCD19_DANRE Protocadherin-19 (Gene Name=pcdh19)