Structure of PDB 6wdd Chain d

Receptor sequence

>6wddd (length=201) Species: 562 (Escherichia coli) [Search protein sequence]

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

3D structure

PDB

6wdd Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.

Chain

Resolution

3.2 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	d	N24 H29 V33 Y35 A36 G38 R40 Q41 T43 R44 A45 Q46 K47 R49 A50 V52 T53 G54 S55 K57 K58 Q62 K63 G64 T65 R67 A68 R69 G71 P76 I77 W78 R79 T84 F85 Q94 K95 N97 K98 Y101 K130 T131 K132 L159 R162 N163 H165 M199	N24 H29 V33 Y35 A36 G38 R40 Q41 T43 R44 A45 Q46 K47 R49 A50 V52 T53 G54 S55 K57 K58 Q62 K63 G64 T65 R67 A68 R69 G71 P76 I77 W78 R79 T84 F85 Q94 K95 N97 K98 Y101 K130 T131 K132 L159 R162 N163 H165 M199

Gene Ontology

	Molecular Function
GO:0001070	RNA-binding transcription regulator activity
GO:0003677	DNA binding
GO:0003735	structural constituent of ribosome
GO:0005515	protein binding
GO:0019843	rRNA binding
GO:0030371	translation repressor activity
GO:0048027	mRNA 5'-UTR binding
GO:0060698	endoribonuclease inhibitor activity

	Biological Process
GO:0002181	cytoplasmic translation
GO:0006353	DNA-templated transcription termination
GO:0006412	translation
GO:0006417	regulation of translation
GO:0017148	negative regulation of translation
GO:0031555	transcriptional attenuation
GO:0042255	ribosome assembly
GO:0045892	negative regulation of DNA-templated transcription
GO:0046677	response to antibiotic
GO:2000766	negative regulation of cytoplasmic translation

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005840	ribosome
GO:0015934	large ribosomal subunit
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:6wdd, PDBe:6wdd, PDBj:6wdd
PDBsum	6wdd
PubMed	32612237
UniProt	P60723\|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)

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