Structure of PDB 5dzy Chain D

Receptor sequence

>5dzyD (length=412) Species: 10090 (Mus musculus)

AISYSMPEETESGYLVANLAQDLGLRVGELTTRGARIHHNGNKELLQLDA
ERGNLLLKEKPDREALCGATEPCVLHFQIILENPVQFFQTDLQFTDINDH
FPEFPDTEMLLKIQEIAQPGTVFPLKAAQDPDIGSNAVQNYTVSPNLHFH
VVTLSRSDDRKYPELVLDRALDREEQPELTLILTALDGGAPPKSGTTTVR
IEVVDINDNAPQFLQSLYAVEVPENSPLNALVVTVSARDLDAGIHGNVAY
SLFQGGGGPQPFVIDEITGEIRLKGALDFEATSYYTMEIVATDSGGLSGK
CTVAIQVLDVNDNAPKLTISSLTSSIPENAPEAVVAVFSVSDPDSGDNGR
MVCSIQNGLPFLLKPTFKNFYTLVTERPLDRESNAEYNITITVSDLGTPR
LTTQHTITVQVS

3D structure

• PDB: 5dzy Structural Basis of Diverse Homophilic Recognition by Clustered alpha- and beta-Protocadherins.
• Chain: D
• Resolution: 2.9 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	FUC	D	T143 L187	T142 L186
BS02	MAN	D	I183 T199	I182 T198
BS03	CA	D	D63 E65 D100 H101	D62 E64 D99 H100
BS04	CA	D	E9 E65 D97 I98 D100 D133	E8 E64 D96 I97 D99 D132
BS05	CA	D	N99 H101 D131 D133 D188	N98 H100 D130 D132 D187
BS06	CA	D	E116 D173 E175 D209	E115 D172 E174 D208
BS07	CA	D	E116 E175 D206 I207 D209 D242	E115 E174 D205 I206 D208 D241
BS08	CA	D	N208 N210 D240 D242 H246 D294	N207 N209 D239 D241 H245 D293
BS09	CA	D	E225 D279 E281 D313	E224 D278 E280 D312
BS10	CA	D	E225 E281 D310 V311 D313 D345	E224 E280 D309 V310 D312 D344
BS11	CA	D	N312 N314 D343 D345 N349 D396	N311 N313 D342 D344 N348 D395

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:5dzy, PDBe:5dzy, PDBj:5dzy
• PDBsum: 5dzy
• PubMed: 27161523
• UniProt: Q91XZ2|PCDB8_MOUSE Protocadherin beta-8 (Gene Name=Pcdhb8)