Structure of PDB 1vy5 Chain BD

Receptor sequence
>1vy5BD (length=275) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARRKK
3D structure
PDB1vy5 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
ChainBD
Resolution2.55 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 BD Q166 K202 Q165 K201
BS02 rna BD K7 P8 Y9 T10 S12 R13 R14 F15 F21 E28 K31 K35 P36 K38 K39 T40 G42 R43 N44 N45 Q46 G47 R48 I49 T50 V51 R52 R54 G55 G56 H58 K59 R60 L61 Y62 R63 Y84 P86 N87 R88 D99 G100 E101 K102 L147 E148 K150 K151 K154 L155 A156 R157 A158 A159 G160 T161 Y172 L177 P178 S179 E181 R183 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 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 S266 R268 F269 R273 R274 K6 P7 Y8 T9 S11 R12 R13 F14 F20 E27 K30 K34 P35 K37 K38 T39 G41 R42 N43 N44 Q45 G46 R47 I48 T49 V50 R51 R53 G54 G55 H57 K58 R59 L60 Y61 R62 Y83 P85 N86 R87 D98 G99 E100 K101 L146 E147 K149 K150 K153 L154 A155 R156 A157 A158 G159 T160 Y171 L176 P177 S178 E180 R182 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 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 S265 R267 F268 R272 R273
BS03 MG BD H220 R222 H219 R221
BS04 MG BD K5 F6 R13 R14 K4 F5 R12 R13
BS05 MG BD D85 A90 R91 D84 A89 R90
BS06 MG BD G235 G236 G238 G234 G235 G237
BS07 MG BD H58 R60 W214 L215 H57 R59 W213 L214
BS08 MG BD F21 R91 F20 R90
BS09 MG BD G41 V51 R52 F53 R54 G40 V50 R51 F52 R53
BS10 MG BD R244 P245 R243 P244
BS11 MG BD E181 R273 R274 E180 R272 R273
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1vy5, PDBe:1vy5, PDBj:1vy5
PDBsum1vy5
PubMed25132179
UniProtP60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)

[Back to BioLiP]