Structure of PDB 8v87 Chain B

Receptor sequence

>8v87B (length=336) Species: 1247190 (Saccharomyces cerevisiae BY4741) [Search protein sequence]

GHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLD
RPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLS
DEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVL
VHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQ
NEMIDAIAVTKGHGFEGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

3D structure

PDB

8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.

Chain

Resolution

2.66 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	H13 L14 G15 F16 L17 P18 R19 K20 R21 I25 R26 R28 K30 A31 M53 T54 T55 R62 G64 S65 A75 Y92 T95 R97 L99 R100 S101 L102 T103 T104 W106 R116 R117 F118 Y119 K120 N121 Y123 K124 S125 K126 K128 A129 F130 K132 Y133 R150 Y154 R159 Q173 K174 K175 E180 T221 K222 G223 G225 F226 E227 Q269 Y272 S274 R275 T276 N279 M308 G309 H313 Y314 G315 E316 K325 C327 I328 G330 N331 K333 R334 L342 Y343 R348 K349 S363 K364 F365 G366 K367 K376 M380 L383 K384	H2 L3 G4 F5 L6 P7 R8 K9 R10 I14 R15 R17 K19 A20 M42 T43 T44 R51 G53 S54 A64 Y81 T84 R86 L88 R89 S90 L91 T92 T93 W95 R105 R106 F107 Y108 K109 N110 Y112 K113 S114 K115 K117 A118 F119 K121 Y122 R139 Y143 R148 Q162 K163 K164 E169 T210 K211 G212 G214 F215 E216 Q218 Y221 S223 R224 T225 N228 M257 G258 H262 Y263 G264 E265 K274 C276 I277 G279 N280 K282 R283 L291 Y292 R297 K298 S312 K313 F314 G315 K316 K325 M329 L332 K333

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0005515	protein binding

	Biological Process
GO:0000027	ribosomal large subunit assembly
GO:0002181	cytoplasmic translation
GO:0006364	rRNA processing
GO:0006412	translation
GO:0006414	translational elongation
GO:1990145	maintenance of translational fidelity

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

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Molecular Function

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Cellular Component

External links

PDB	RCSB:8v87, PDBe:8v87, PDBj:8v87
PDBsum	8v87
PubMed	38632236
UniProt	P14126\|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)

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