Structure of PDB 8pvk Chain LD

Receptor sequence

>8pvkLD (length=286) Species: 759272 (Thermochaetoides thermophila DSM 1495)

KLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAKNKYNAPKYRLVVR
FTNRDIITQMVTSEINGDKIFAAAYSHELRAYGINHGLTNWAAAYATGLL
LARRVLAKLGLDGEYTLTEAAETEDGERRPFKAILDVGLARTSTGARVFG
VMKGASDGGIFIPHSENRFPGYDIETEELDTEVLKKYIYGGHVAEYMETL
ADDDEERYKSQFVKYIEDDVEADSLEELYAEAHKQIRADPFRKYVSDAPK
KSKEEWKAESLKYKKAKLSREERKARVEAKIKQLLA

3D structure

• PDB: 8pvk Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Chain: LD
• Resolution: 2.55 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	LD	K8 Y12 R15 F16 Q17 K19 R23 T28 D29 Y31 R35 L36 Q39 A40 K41 K48 I148 V151 L153 R155 T156 H178 S179 N181 R182	K4 Y8 R11 F12 Q13 K15 R19 T24 D25 Y27 R31 L32 Q35 A36 K37 K44 I134 V137 L139 R141 T142 H164 S165 N167 R168
BS02	rna	LD	K8 S10 Y13 S14 F16 T18 F20 K21 R22 R24 T28 Y30 R33 R50 R54 T56 N57 R58 I61 Q63 N70 G71 D72 K73 I74 Y79 H90 G91 N94 W95 R155 T158 G159 A160 R161 Y201 H206 Y210 R221 Q225 K228 Y229 P263 K264 K267 W270 K271 S274 Y277 K278 K279 K281 L282 R284 R287 R290	K4 S6 Y9 S10 F12 T14 F16 K17 R18 R20 T24 Y26 R29 R46 R50 T52 N53 R54 I57 Q59 N66 G67 D68 K69 I70 Y75 H86 G87 N90 W91 R141 T144 G145 A146 R147 Y187 H192 Y196 R207 Q211 K214 Y215 P249 K250 K253 W256 K257 S260 Y263 K264 K265 K267 L268 R270 R273 R276

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pvk, PDBe:8pvk, PDBj:8pvk
• PDBsum: 8pvk
• PubMed: 37921038
• UniProt: G0SEG2