Structure of PDB 5dzx Chain A

Receptor sequence

>5dzxA (length=414) Species: 10090 (Mus musculus)

IRYSIPEETESGYLVAHLAKDLGFRVGELATRRARIHHRGNKELLQLDVE
TGNLLLKEKPDREALCGATEPCVLHFQIILENPVQFFQTELQLTDINDHS
PEFPDTEMLLKIQESTQPATVFLLKAAQDSDIGSNAVQNYTVSPNLHFHV
VTLSRSDGRKYPELVLDRALDREEQPELTLILTALDGGAPPKSGTTTVRI
EVVDINDNAPEFVQSLYSVEVPENSPLDALVVTVSARDLDAGIHGNVAYS
LFQGGGGPQPFVIDEITGEIRLKGALDFEATSYYTMEIVATDSGGLSGKC
TVAIQVLDVNDNAPKLTISSLTSSIPENAPEAVVAVFSVSDPDSGDNGRM
VCSIQNELPFLLKPTFENYYTLAAEGPLDREIREEYNITIIVSDLGTPRL
TTQHTITVQVVDIN

3D structure

• PDB: 5dzx Structural Basis of Diverse Homophilic Recognition by Clustered alpha- and beta-Protocadherins.
• Chain: A
• Resolution: 2.879 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	E9 E10 D63 E65 D100	E7 E8 D61 E63 D98
BS02	CA	A	E9 E65 D97 I98 D100 D133	E7 E63 D95 I96 D98 D131
BS03	CA	A	N99 H101 D131 D133 N137 D188	N97 H99 D129 D131 N135 D186
BS04	CA	A	E116 D173 E175 D209	E114 D171 E173 D207
BS05	CA	A	E116 E175 D206 I207 D209 D242	E114 E173 D204 I205 D207 D240
BS06	CA	A	N208 N210 D240 D242 H246 D294	N206 N208 D238 D240 H244 D292
BS07	CA	A	E225 D279 E281 D313	E223 D277 E279 D311
BS08	CA	A	E225 E281 D310 V311 D313 D345	E223 E279 D308 V309 D311 D343
BS09	CA	A	N312 N314 D343 D345 N349 D396	N310 N312 D341 D343 N347 D394

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:5dzx, PDBe:5dzx, PDBj:5dzx
• PDBsum: 5dzx
• PubMed: 27161523
• UniProt: Q91XZ4|PCDB6_MOUSE Protocadherin beta-6 (Gene Name=Pcdhb6)