Structure of PDB 5gip Chain B

Receptor sequence

>5gipB (length=375) Species: 2287 (Saccharolobus solfataricus)

KIYLIEHVIGAVAYDENGNIVDYITNPRDLGKITEELLNNEKGIPFSATV
ELLKKVNPQEVVVENEAEVPKLQALGYRVSYEPYSKVSRIFRESLPKVAI
DIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDK
TINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKE
LGFNEQRINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNN
YLEGVMKEVAPNVTALVGPALGARLLSIAGSLDELAKMPASTIQVLGAEK
ALFRALRSGGRPPKHGIIFQYPAIHTSPRWQRGKIARALAAKLAIAARVD
AFSGRFIGDQLNEQLKKRIDEIKEK

3D structure

• PDB: 5gip Box C/D guide RNAs recognize a maximum of 10 nt of substrates
• Chain: B
• Resolution: 3.129 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	rna	B	K152 E159 R160 E163 G299 A300 K302 A303 R313 P314 P315 K316 H317 G318 F321 G335 K336 R339 A343 K344 R370	K150 E157 R158 E161 G297 A298 K300 A301 R311 P312 P313 K314 H315 G316 F319 G333 K334 R337 A341 K342 R368
BS02	rna	B	R145 S293 T294 Q296 E301 F305	R143 S291 T292 Q294 E299 F303
BS03	rna	B	N155 E159 H179 R276 Q322 H327	N153 E157 H177 R274 Q320 H325
BS04	rna	B	K302 R306 R309	K300 R304 R307
BS05	rna	B	I197 N211 K218	I195 N209 K216

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0030515 snoRNA binding

Cellular Component

• GO:0031428 box C/D methylation guide snoRNP complex
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:5gip, PDBe:5gip, PDBj:5gip
• PDBsum: 5gip
• PubMed: 27625427
• UniProt: Q97ZH3