Structure of PDB 4v9r Chain DQ

Receptor sequence

>4v9rDQ (length=141) Species: 274 (Thermus thermophilus)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 4v9r The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.
• Chain: DQ
• Resolution: 3.0 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	DQ	R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 Q46 A49 R56 K63 R67 F69 D71 Y74 K76 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 P126 K128	R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G24 Q46 A49 R56 K63 R67 F69 D71 Y74 K76 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 P126 K128
BS02	rna	DQ	R16 L17 G19	R16 L17 G19
BS03	MG	DQ	G122 I127	G122 I127
BS04	MG	DQ	G84 G86	G84 G86

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:4v9r, PDBe:4v9r, PDBj:4v9r
• PDBsum: 4v9r
• PubMed: 24412368
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)