Structure of PDB 4v83 Chain DD

Receptor sequence

>4v83DD (length=204) Species: 262724 (Thermus thermophilus HB27)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

3D structure

• PDB: 4v83 Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
• Chain: DD
• Resolution: 3.5 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	K8 M11 T12 R13 P22 Q35 R37 K41 D42 Y44 Q48 K57 R58 N60 R61 P62 L63 G65 H66 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 K152 G153 K154 M156 A157 H159 R164 V165 T166 M168 N169 K185 A187 P189 P191 K202 K203	K8 M11 T12 R13 P22 Q35 R37 K41 D42 Y44 Q48 K57 R58 N60 R61 P62 L63 G65 H66 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 K152 G153 K154 M156 A157 H159 R164 V165 T166 M168 N169 K185 A187 P189 P191 K202 K203
BS02	MG	DD	A131 K133	A131 K133
BS03	MG	DD	K118 R119	K118 R119

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:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v83, PDBe:4v83, PDBj:4v83
• PDBsum: 4v83
• PubMed: 21245352
• UniProt: Q72I04|RL3_THET2 Large ribosomal subunit protein uL3 (Gene Name=rplC)