Structure of PDB 5vp2 Chain 11

Receptor sequence

>5vp211 (length=97) Species: 300852 (Thermus thermophilus HB8)

SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 11
• 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	11	S2 K3 K10 I13 V14 A15 N16 I18 Q19 R20 R21 A24 K25 R26 G29 V30 K32 K33 T34 T35 I37 K39 R40 R41 Q42 Y43 P44 N45 Q47 K48 R50 R52 R61 S65 H66 K69 G79 L80	S1 K2 K9 I12 V13 A14 N15 I17 Q18 R19 R20 A23 K24 R25 G28 V29 K31 K32 T33 T34 I36 K38 R39 R40 Q41 Y42 P43 N44 Q46 K47 R49 R51 R60 S64 H65 K68 G78 L79
BS02	MG	11	R20 K32 T34	R19 K31 T33

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)