Structure of PDB 5vp2 Chain 25

Receptor sequence

>5vp225 (length=59) Species: 300852 (Thermus thermophilus HB8)

AKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGY
YAGRKVLEV

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 25
• 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	25	A2 K3 H4 P5 V6 P7 K8 K9 K10 T11 S12 K13 A14 R15 R16 D17 A18 R19 R20 S21 H22 H23 T29 V31 P34 K40 P42 H43 Y52 A53	A1 K2 H3 P4 V5 P6 K7 K8 K9 T10 S11 K12 A13 R14 R15 D16 A17 R18 R19 S20 H21 H22 T28 V30 P33 K39 P41 H42 Y51 A52
BS02	MG	25	V31 P32	V30 P31
BS03	ZN	25	C33 C36 C46 C49	C32 C35 C45 C48

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P80339|RL32_THET8 Large ribosomal subunit protein bL32 (Gene Name=rpmF)