Structure of PDB 1q3v Chain F

Receptor sequence

>1q3vF (length=322) Species: 10678 (Punavirus P1)

SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPE
DVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRR
IRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYN
TLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTK
LVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATH
RLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVN
IVMNYIRNLDSETGAMVRLLED

3D structure

• PDB: 1q3v Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation
• Chain: F
• Resolution: 2.91 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	F	M44 S47 R50 R81 L83 A84 K86 T87 Q90 A131 K132 Q156 R159 R173 K201 R241 V242 K244 L256 S257 R259 R282 Y283 R292 W315 Y324	M25 S28 R31 R62 L64 A65 K67 T68 Q71 A112 K113 Q137 R140 R154 K182 R222 V223 K225 L237 S238 R240 R263 Y264 R273 W296 Y305
BS02	dna	F	K122 K201 T202 T316 N317 N319 I320	K103 K182 T183 T297 N298 N300 I301
BS03	dna	F	F37 S38 H40 T41 M97 R100 R101 R106 R121 I174 A175 K201 K244 N245 R259 E262 K276 R282 Y283 S287 G288 H289	F18 S19 H21 T22 M78 R81 R82 R87 R102 I155 A156 K182 K225 N226 R240 E243 K257 R263 Y264 S268 G269 H270

Gene Ontology

Molecular Function

• GO:0003677 DNA binding

Biological Process

• GO:0006310 DNA recombination
• GO:0015074 DNA integration

External links

• PDB: RCSB:1q3v, PDBe:1q3v, PDBj:1q3v
• PDBsum: 1q3v
• PubMed: 12954782
• UniProt: P06956|RECR_BPP1 Recombinase cre (Gene Name=cre)