Structure of PDB 1vy7 Chain DD

Receptor sequence

>1vy7DD (length=275) Species: 300852 (Thermus thermophilus HB8)

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARRKK

3D structure

• PDB: 1vy7 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: DD
• Resolution: 2.8 Å

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	DD	Q166 K202	Q165 K201
BS02	rna	DD	K7 P8 Y9 T10 P11 S12 R13 R14 F15 F21 E28 K31 P36 L37 K38 K39 T40 G42 R43 N44 N45 Q46 G47 R48 I49 T50 V51 R52 R54 G56 H58 K59 R60 L61 Y62 R63 Y84 P86 R88 D99 G100 E101 K102 L147 E148 P149 K150 K151 K154 L155 A156 R157 A158 A159 T161 Y172 L177 P178 S179 E181 R183 H186 A199 H201 K202 V205 L206 G207 K208 A209 G210 R211 S212 R213 W214 R218 P219 H220 V221 R222 G223 A224 A225 M226 N227 P228 V229 D230 H231 H233 G235 G236 E237 G238 R239 A240 P241 R242 G243 R244 P246 A247 S248 P249 W250 W252 Q253 T254 K255 G256 L257 K258 T259 R260 K261 R263 K264 P265 S266 R268 F269 R273 R274	K6 P7 Y8 T9 P10 S11 R12 R13 F14 F20 E27 K30 P35 L36 K37 K38 T39 G41 R42 N43 N44 Q45 G46 R47 I48 T49 V50 R51 R53 G55 H57 K58 R59 L60 Y61 R62 Y83 P85 R87 D98 G99 E100 K101 L146 E147 P148 K149 K150 K153 L154 A155 R156 A157 A158 T160 Y171 L176 P177 S178 E180 R182 H185 A198 H200 K201 V204 L205 G206 K207 A208 G209 R210 S211 R212 W213 R217 P218 H219 V220 R221 G222 A223 A224 M225 N226 P227 V228 D229 H230 H232 G234 G235 E236 G237 R238 A239 P240 R241 G242 R243 P245 A246 S247 P248 W249 W251 Q252 T253 K254 G255 L256 K257 T258 R259 K260 R262 K263 P264 S265 R267 F268 R272 R273
BS03	MG	DD	H220 R222	H219 R221
BS04	MG	DD	P241 R242	P240 R241
BS05	MG	DD	W214 L215	W213 L214
BS06	MG	DD	G235 G236 G238 R239	G234 G235 G237 R238
BS07	MG	DD	F53 R54	F52 R53
BS08	MG	DD	P11 R14	P10 R13

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

External links

• PDB: RCSB:1vy7, PDBe:1vy7, PDBj:1vy7
• PDBsum: 1vy7
• PubMed: 25132179
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)