Structure of PDB 8v87 Chain b

Receptor sequence

>8v87b (length=469) Species: 1247190 (Saccharomyces cerevisiae BY4741) [Search protein sequence]

QLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVK
YTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRA
KSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYLE
QVRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFTT
KSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCVL
YFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDEE
RAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKSQ
SRINNVLNKIHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARD
IEAENGGAGVFNVNLKDKYLLEDDEWKNDIMPEILDGKNVYDFLDPEIAA
KLQALEEEEEKLENEGFYN

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	K6 D19 I20 L22 N23 Q26 R27 K28 P30 T31 V32 I33 R34 G36 F37 R41 R48 K49 P69 N70 N89 Y91 K92 L95 A96 S99 R100 S103 L104 Q107 F123 K126 K129 R130 A131 L133 G134 R135 I139 K142 R159 S162 S190 Y197 F199 K202 H208 R227 G410 V411	K5 D18 I19 L21 N22 Q25 R26 K27 P29 T30 V31 I32 R33 G35 F36 R40 R47 K48 P68 N69 N88 Y90 K91 L94 A95 S98 R99 S102 L103 Q106 F122 K125 K128 R129 A130 L132 G133 R134 I138 K141 R158 S161 S189 Y196 F198 K201 H207 R226 G409 V410
BS02	GDP	b	N177 V178 G179 K180 S181 Q195 N288 K289 C322	N176 V177 G178 K179 S180 Q194 N287 K288 C321

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003924	GTPase activity
GO:0005515	protein binding
GO:0005525	GTP binding

	Biological Process
GO:0000054	ribosomal subunit export from nucleus
GO:0006364	rRNA processing
GO:0042254	ribosome biogenesis
GO:0042273	ribosomal large subunit biogenesis
GO:1902626	assembly of large subunit precursor of preribosome

	Cellular Component
GO:0005634	nucleus
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0030687	preribosome, large subunit precursor

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8v87, PDBe:8v87, PDBj:8v87
PDBsum	8v87
PubMed	38632236
UniProt	Q02892\|NOG1_YEAST Nucleolar GTP-binding protein 1 (Gene Name=NOG1)

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