Structure of PDB 6ndk Chain YF

Receptor sequence

>6ndkYF (length=202) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

PDB

6ndk Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing intRNACGGProfor decoding

Chain

Resolution

3.64 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	YF	N29 H31 W34 E35 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 K52 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 R74 H75 G76 I82 F83 V84 G85 F90 G91 P92 R95 Y99 T100 P102 K103 K104 R106 K135 T136 R165 R168 N169 P171 E179 G180 N182 Y184 R205	N24 H26 W29 E30 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 K47 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 R69 H70 G71 I77 F78 V79 G80 F85 G86 P87 R90 Y94 T95 P97 K98 K99 R101 K130 T131 R160 R163 N164 P166 E174 G175 N177 Y179 R200
BS02	MG	YF	V57 A58 Y59	V52 A53 Y54

Gene Ontology

	Molecular Function
GO:0003735	structural constituent of ribosome
GO:0019843	rRNA binding

	Biological Process
GO:0006412	translation

	Cellular Component
GO:0005840	ribosome
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:6ndk, PDBe:6ndk, PDBj:6ndk
PDBsum	6ndk
PubMed	30782843
UniProt	Q5SHN9\|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)

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