Structure of PDB 8qoa Chain f

Receptor sequence

>8qoaf (length=177) Species: 679895 (Escherichia coli BW25113)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR

3D structure

• PDB: 8qoa SecM adopts alpha-helical conformation in the ribosomal exit tunnel and traps a pre-peptide bond formation state of the ribosome
• Chain: f
• Resolution: 2.0 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	f	S73 A75 R80	S72 A74 R79
BS02	rna	f	S24 M26 Q27 Q63 K64 L66 K69 V89 T90 R92	S23 M25 Q26 Q62 K63 L65 K68 V88 T89 R91
BS03	rna	f	K33 T35 N37 M38 G39 G41 T68 A70 R71 V74 F77 I79 I85 K88 S121 D123 R125 N127 S129 M130 G131 G151 L152 D153 T155	K32 T34 N36 M37 G38 G40 T67 A69 R70 V73 F76 I78 I84 K87 S120 D122 R124 N126 S128 M129 G130 G150 L151 D152 T154

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qoa, PDBe:8qoa, PDBj:8qoa
• PDBsum: 8qoa
• PubMed: 38503753
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)