Structure of PDB 5vp2 Chain 2m

Receptor sequence

>5vp22m (length=122) Species: 300852 (Thermus thermophilus HB8)

RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAE
VVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQR
TRTNARTRKGPRKTVAGKKKAP

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 2m
• 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	2m	R14 V17 Y21 Y23 G24 I25 G26 A28 R29 R44 V74 N77 I78 Y87 R88 R91 H92 P97 V98 R99 Q101 R102 T103 R104 T105 N106 A107 R108 T109 R110 K111 R114 K115 T116 V117	R12 V15 Y19 Y21 G22 I23 G24 A26 R27 R42 V72 N75 I76 Y85 R86 R89 H90 P95 V96 R97 Q99 R100 T101 R102 T103 N104 A105 R106 T107 R108 K109 R112 K113 T114 V115
BS02	rna	2m	K120 A123	K118 A121
BS03	rna	2m	A118 G119	A116 G117

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)