Structure of PDB 1vy4 Chain DE

Receptor sequence

>1vy4DE (length=204) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

3D structure

• PDB: 1vy4 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: DE
• Resolution: 2.6 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	DE	K8 M11 T12 R13 P22 Q35 R37 K41 D42 Y44 R58 N60 R61 P62 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 L170 K185 G186 A187 V188 P189 G190 P191 N192 K202 K203 A204	K8 M11 T12 R13 P22 Q35 R37 K41 D42 Y44 R58 N60 R61 P62 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 L170 K185 G186 A187 V188 P189 G190 P191 N192 K202 K203 A204
BS02	MG	DE	M117 R136	M117 R136
BS03	MG	DE	R119 Y160	R119 Y160

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:1vy4, PDBe:1vy4, PDBj:1vy4
• PDBsum: 1vy4
• PubMed: 25132179
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)