Structure of PDB 1vy5 Chain B1

Receptor sequence

>1vy5B1 (length=97) Species: 300852 (Thermus thermophilus HB8)

SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL

3D structure

• PDB: 1vy5 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: B1
• Resolution: 2.55 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	B1	K23 V30	K22 V29
BS02	rna	B1	S2 K3 K10 R11 I13 V14 A15 N16 I18 R20 R21 A24 K25 G28 G29 V30 K32 K33 T35 K39 R40 R41 Q42 Y43 P44 N45 Q47 R50 R52 R61 S65 H66 K69 R76 G79 L80	S1 K2 K9 R10 I12 V13 A14 N15 I17 R19 R20 A23 K24 G27 G28 V29 K31 K32 T34 K38 R39 R40 Q41 Y42 P43 N44 Q46 R49 R51 R60 S64 H65 K68 R75 G78 L79
BS03	MG	B1	K32 K33 T34	K31 K32 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:1vy5, PDBe:1vy5, PDBj:1vy5
• PDBsum: 1vy5
• PubMed: 25132179
• UniProt: P60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)