Structure of PDB 1vy5 Chain BF

Receptor sequence

>1vy5BF (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

• PDB: 1vy5 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: BF
• 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	BF	N29 H31 L32 W34 E35 R38 Q40 L41 A42 K43 R44 R45 R46 T48 A49 S50 T51 K52 T53 R54 G55 V57 A58 Y59 S60 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 V105 R106 K108 G134 K135 T136 K137 R165 R168 N169 L170 P171 E179 G180 N182 Y184 R205	N24 H26 L27 W29 E30 R33 Q35 L36 A37 K38 R39 R40 R41 T43 A44 S45 T46 K47 T48 R49 G50 V52 A53 Y54 S55 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 V100 R101 K103 G129 K130 T131 K132 R160 R163 N164 L165 P166 E174 G175 N177 Y179 R200
BS02	MG	BF	R72 A73	R67 A68
BS03	MG	BF	T51 K52	T46 K47
BS04	MG	BF	G61 R62	G56 R57
BS05	MG	BF	S50 T51	S45 T46
BS06	MG	BF	V89 F90	V84 F85
BS07	MG	BF	G76 D77	G71 D72
BS08	MG	BF	A58 Y59	A53 Y54
BS09	MG	BF	K63 W65 P66 R74 H75	K58 W60 P61 R69 H70
BS10	MG	BF	R54 D77	R49 D72

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

External links

• PDB: RCSB:1vy5, PDBe:1vy5, PDBj:1vy5
• PDBsum: 1vy5
• PubMed: 25132179
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)