Structure of PDB 5fdv Chain 1F

Receptor sequence

>5fdv1F (length=202) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

PDB

5fdv Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.

Chain

Resolution

2.8 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	1F	N29 H31 L32 W34 E35 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 P81 I82 F83 V84 G85 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 R106 K108 G134 K135 T136 R165 R168 N169 L170 P171 L176 E179 G180 N182 Y184 R205	N24 H26 L27 W29 E30 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 K47 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 A68 R69 H70 G71 P76 I77 F78 V79 G80 V84 F85 P87 P89 R90 Y94 T95 P97 K98 K99 R101 K103 G129 K130 T131 R160 R163 N164 L165 P166 L171 E174 G175 N177 Y179 R200
BS02	MG	1F	S50 T51	S45 T46
BS03	MG	1F	T51 K52	T46 K47
BS04	MG	1F	H75 G76 D77	H70 G71 D72
BS05	MG	1F	R45 R46 G47	R40 R41 G42
BS06	MG	1F	R72 A73	R67 A68
BS07	MG	1F	R168 L170	R163 L165
BS08	MG	1F	G47 A49 Y97	G42 A44 Y92
BS09	MG	1F	Y59 S60 D77 G79	Y54 S55 D72 G74
BS10	MG	1F	K63 W65 P66 R74 H75	K58 W60 P61 R69 H70
BS11	MG	1F	R54 D77	R49 D72
BS12	MG	1F	A58 Y59	A53 Y54
BS13	MG	1F	K63 G76	K58 G71

Gene Ontology

	Molecular Function
GO:0003735	structural constituent of ribosome
GO:0019843	rRNA binding

	Biological Process
GO:0006412	translation

	Cellular Component
GO:0005840	ribosome
GO:1990904	ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5fdv, PDBe:5fdv, PDBj:5fdv
PDBsum	5fdv
PubMed	26792896
UniProt	Q5SHN9\|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)

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