Structure of PDB 8ipd Chain w

Receptor sequence

>8ipdw (length=433) Species: 9606 (Homo sapiens)

SKASTNPDRVQGAGGQNMRDRATIRRLNMYRQKERRNSRGKIIKPLQYQS
TVASGTVARVEPNIKWFGNTRVIKQSSLQKFQEEMDTVMSKLPMSLNLKV
HILDTESFETTFGPKSQRKRPNLFASDMQSLIENAEMSTESYDQGKDRDL
VTEDTGVRNEAQEEIYKKGQSKRIWGELYKVIDSSDVVVQVLDARDPMGT
RSPHIETYLKKEKPWKHLIFVLNKCDLVPTWATKRWVAVLSQDYPTLAFH
ASLTNPFGKGAFIQLLRQFGKLHTDKKQISVGFIGYPNVGKSSVINTLRS
KKVCNVAPIAGETKVWQYITLMRRIFLIDCPGVVYPSEDSETDIVLKGVV
QVEKIKSPEDHIGAVLERAKPEYISKTYKIDSWENAEDFLEKLAFRTGKL
LKGGEPDLQTVGKMVLNDWQRGRIPFFVKPPNA

3D structure

• PDB: 8ipd Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Chain: w
• Resolution: 3.2 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	w	K16 T19 Q30 N31 M32 R33 R40 N51 R53 S68 G69 K131 H133 I134 K147 Q149 K151 R180 E196 K200 Q202 S203 K204 R205 I206 W207 P288 K291 I295 R299 V335 G343 V347 W348 Q349 Y350 I351 T352 M354 R355 Q383 E385 K386 R428 T429 K431 L432 L433 G435 Q441 T442 M446 R453	K2 T5 Q16 N17 M18 R19 R26 N37 R39 S54 G55 K99 H101 I102 K115 Q117 K119 R148 E164 K168 Q170 S171 K172 R173 I174 W175 P256 K259 I263 R267 V303 G311 V315 W316 Q317 Y318 I319 T320 M322 R323 Q351 E353 K354 R396 T397 K399 L400 L401 G403 Q409 T410 M414 R421
BS02	GTP	w	D258 H282 A283 P319 N320 G322 K323 S324 S325 V338 A339	D226 H250 A251 P287 N288 G290 K291 S292 S293 V306 A307

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005525 GTP binding

Biological Process

• GO:0008150 biological_process
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0016020 membrane

External links

• PDB: RCSB:8ipd, PDBe:8ipd, PDBj:8ipd
• PDBsum: 8ipd
• PubMed: 37491604
• UniProt: Q13823|NOG2_HUMAN Nucleolar GTP-binding protein 2 (Gene Name=GNL2)