Structure of PDB 5vp2 Chain 1R

Receptor sequence

>5vp21R (length=118) Species: 300852 (Thermus thermophilus HB8)

MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDH
LIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKL
AERRRGDGAPLALVELVE

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 1R
• 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	1R	M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 H16 R17 A19 R22 N23 Q24 K26 S27 H31 I34 T35 T36 T37 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 R68 Q71 R77 R90 Q91 G92 G93 R96 K99 R104 R105 G106 D107	M1 R2 H3 L4 K5 S6 R8 K9 N11 R12 H13 S14 H16 R17 A19 R22 N23 Q24 K26 S27 H31 I34 T35 T36 T37 P39 K40 K42 R45 D49 H50 H53 R57 L60 H61 R63 R64 R68 Q71 R77 R90 Q91 G92 G93 R96 K99 R104 R105 G106 D107
BS02	MG	1R	R105 G106	R105 G106
BS03	MG	1R	L98 K99	L98 K99

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: Q9Z9H5|RL17_THET8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)