Structure of PDB 5y3m Chain B

Receptor sequence

>5y3mB (length=732) Species: 9913 (Bos taurus)

LPAFLPCELQPHGQVDCNWLFLKSVPHFSAGAPRANVTSLSLISNRIHHL
HDSDFVHLSNLRVLNLKWNCPPAGLSPMHFPCRMTIEPNTFLAVPTLEEL
NLSYNGITTVPALPSSLVSLSLSHTSILVLGPTHFTGLHALRFLYMDGNC
YYMNPCPRALEVAPGALLGLGNLTHLSLKYNNLTEVPRRLPPSLDTLLLS
YNHIVTLAPEDLANLTALRVLDVGGNCRRCDHARNPCRECPKNFPKLHPD
TFSHLSRLEGLVLKDSSLYKLEKDWFRGLGRLQVLDLSENFLYDYITKTT
IFNDLTQLRRLNLSFNYHKKVSFAHLHLASSFGSLVSLEKLDMHGIFFRS
LTNITLQSLTRLPKLQSLHLQLNFINQAQLSIFGAFPSLLFVDLSDNRIS
SCNLNFTLDLSRNNLVTIQQEMFTRLSRLQCLRLSHNSISQAVNGSQFVP
LTSLRVLDLSHNKLDLYHGRSFTELPQLEALDLSYNSQPFSMQGVGHNLS
FVAQLPSLRYLSLAHNGIHSRVSQKLSSASLRALDFSGNSLSQMWAEGDL
YLCFFKGLRNLVQLDLSENHLHTLLPRHLDNLPKSLRQLRLRDNNLAFFN
WSSLTVLPRLEALDLAGNQLKALSNGSLPPGIRLQKLDVSSNSIGFVIPG
FFVRATRLIELNLSANALKTVDPSWFGSLAGTLKILDVSANPLHCAAFVD
FLLERQEAVPGLSRRVTCGSPGQLQGRSIFTQ

3D structure

• PDB: 5y3m Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation
• Chain: B
• Resolution: 2.5 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	dna	B	D532 Y534 G563 H564 R588 V589	D465 Y467 G496 H497 R521 V522
BS02	dna	B	D258 Y344 H345 K347 V348 S349 F350 A351 F374 R376 F401	D231 Y317 H318 K320 V321 S322 F323 A324 F347 R349 F374
BS03	dna	B	W46 R73 W95 P98 S103 P104 M105 F107	W19 R46 W68 P71 S76 P77 M78 F80
BS04	dna	B	H639 F665	H572 F598

Gene Ontology

Molecular Function

• GO:0004888 transmembrane signaling receptor activity

Biological Process

• GO:0002224 toll-like receptor signaling pathway
• GO:0006955 immune response

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:5y3m, PDBe:5y3m, PDBj:5y3m
• PDBsum: 5y3m
• PubMed: 29625894
• UniProt: Q5I2M5|TLR9_BOVIN Toll-like receptor 9 (Gene Name=TLR9)