Structure of PDB 6ndk Chain YD

Receptor sequence

>6ndkYD (length=275) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARRKK

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)
BS01	rna	YD	K4 K7 Y9 T10 S12 R13 R14 F15 F21 K35 P36 K38 K39 T40 G42 R43 N44 N45 Q46 G47 R48 I49 T50 R52 R54 G56 H58 K59 R60 L61 Y62 R63 K68 Y84 P86 R88 V98 D99 G100 L147 E148 K151 K154 L155 A156 R157 A158 A159 G160 T161 Y172 L177 P178 S179 E181 R183 H186 A199 H201 K202 L206 G207 K208 A209 G210 R211 R213 W214 R217 R218 P219 H220 V221 R222 G223 A225 M226 N227 P228 V229 D230 H231 H233 G235 G236 E237 G238 R239 A240 P241 R242 G243 R244 P246 A247 P249 W250 W252 Q253 T254 K255 G256 L257 K258 T259 R260 K261 R263 K264 P265 S266 R268 F269 R273 R274	K3 K6 Y8 T9 S11 R12 R13 F14 F20 K34 P35 K37 K38 T39 G41 R42 N43 N44 Q45 G46 R47 I48 T49 R51 R53 G55 H57 K58 R59 L60 Y61 R62 K67 Y83 P85 R87 V97 D98 G99 L146 E147 K150 K153 L154 A155 R156 A157 A158 G159 T160 Y171 L176 P177 S178 E180 R182 H185 A198 H200 K201 L205 G206 K207 A208 G209 R210 R212 W213 R216 R217 P218 H219 V220 R221 G222 A224 M225 N226 P227 V228 D229 H230 H232 G234 G235 E236 G237 R238 A239 P240 R241 G242 R243 P245 A246 P248 W249 W251 Q252 T253 K254 G255 L256 K257 T258 R259 K260 R262 K263 P264 S265 R267 F268 R272 R273
BS02	MG	YD	H233 G234	H232 G233
BS03	MG	YD	P11 R14	P10 R13
BS04	MG	YD	Y62 R63 D85 N87 R88	Y61 R62 D84 N86 R87

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0016740	transferase activity
GO:0019843	rRNA binding

	Biological Process
GO:0002181	cytoplasmic translation
GO:0006412	translation

	Cellular Component
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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Biological Process

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Cellular Component

External links

PDB	RCSB:6ndk, PDBe:6ndk, PDBj:6ndk
PDBsum	6ndk
PubMed	30782843
UniProt	P60405\|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)

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