Structure of PDB 5t62 Chain a

Receptor sequence

>5t62a (length=203) Species: 559292 (Saccharomyces cerevisiae S288C)

GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRL
GYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRAT
AEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWI
CDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWR
YRK

3D structure

• PDB: 5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
• Chain: a
• Resolution: 3.3 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	a	G2 Y4 K5 E8 R12 K14 Q15 W28 R31 N34 V35 R41 R44 K47 R49 R50 K54 A55 Q57 R67 R68 G69 N70 R71 K72 K77 Y81 G82 K83 P84 T85 N86 Q87 N90 E91 K93 Y94 Q95 R96 R105 R108 N112 N117 W120 S125 Y127 K128 H139 K140 R147 W150 K157 H158 A161 R162 L164 A166 K169 K170 S171 R172 I174 K176 H178 K179 F180 N182 R187 R188 K189 W191 K192 R193 Q194 W200 Y202 R203 K204	G1 Y3 K4 E7 R11 K13 Q14 W27 R30 N33 V34 R40 R43 K46 R48 R49 K53 A54 Q56 R66 R67 G68 N69 R70 K71 K76 Y80 G81 K82 P83 T84 N85 Q86 N89 E90 K92 Y93 Q94 R95 R104 R107 N111 N116 W119 S124 Y126 K127 H138 K139 R146 W149 K156 H157 A160 R161 L163 A165 K168 K169 S170 R171 I173 K175 H177 K178 F179 N181 R186 R187 K188 W190 K191 R192 Q193 W199 Y201 R202 K203
BS02	rna	a	R38 Q57 V60 Y62 R109 N112 D136	R37 Q56 V59 Y61 R108 N111 D135

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P05748|RL15A_YEAST Large ribosomal subunit protein eL15A (Gene Name=RPL15A)