Structure of PDB 5vpo Chain XD

Receptor sequence

>5vpoXD (length=208) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

PDB

5vpo Mechanism of tRNA-mediated +1 ribosomal frameshifting.

Chain

Resolution

3.34 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	XD	G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 E24 R25 R35 R36 Y38 P40 G41 Q42 H43 R49 S52 Y54 A55 R59 K61 Q62 E72 R73 Q74 K86 V112 S113 R115 Q116 R118 Q119 R122 H123 H125 R132 D134 L135 S137 E205 S208	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 E23 R24 R34 R35 Y37 P39 G40 Q41 H42 R48 S51 Y53 A54 R58 K60 Q61 E71 R72 Q73 K85 V111 S112 R114 Q115 R117 Q118 R121 H122 H124 R131 D133 L134 S136 E204 S207
BS02	ZN	XD	K22 C31	K21 C30

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0019843	rRNA binding
GO:0046872	metal ion binding

	Biological Process
GO:0006412	translation
GO:0042274	ribosomal small subunit biogenesis

	Cellular Component
GO:0005840	ribosome
GO:0015935	small ribosomal subunit
GO:1990904	ribonucleoprotein complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:5vpo, PDBe:5vpo, PDBj:5vpo
PDBsum	5vpo
PubMed	30262649
UniProt	P80373\|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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