Structure of PDB 5fdv Chain 1m

Receptor sequence

>5fdv1m (length=116) Species: 300852 (Thermus thermophilus HB8)

ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEA
EVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQ
RTRTNARTRKGPRKTV

3D structure

• PDB: 5fdv Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Chain: 1m
• 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	1m	D83 R93	D82 R92
BS02	rna	1m	K13 R14 V17 Y21 Y23 G24 I25 G26 A28 R29 R44 Y87 R88 R91 H92 P97 V98 R99 G100 Q101 R102 T103 R104 T105 N106 A107 R108 T109 R110 K111 K115 V117	K12 R13 V16 Y20 Y22 G23 I24 G25 A27 R28 R43 Y86 R87 R90 H91 P96 V97 R98 G99 Q100 R101 T102 R103 T104 N105 A106 R107 T108 R109 K110 K114 V116
BS03	MG	1m	T20 I22 I25	T19 I21 I24

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:5fdv, PDBe:5fdv, PDBj:5fdv
• PDBsum: 5fdv
• PubMed: 26792896
• UniProt: P80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)