Structure of PDB 4v8q Chain BZ

Receptor sequence

>4v8qBZ (length=377) Species: 300852 (Thermus thermophilus HB8)

GEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPHVEYETAKRHYS
HVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGV
PYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLA
LEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDV
FTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQ
EGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEG
GRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPV
ALEEGLRFAIREGGRTVGAGVVTKILE

3D structure

• PDB: 4v8q Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.
• Chain: BZ
• Resolution: 3.1 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	BZ	H19 H85	H17 H57
BS02	rna	BZ	T232 G233 R234 R291	T204 G205 R206 R263
BS03	rna	BZ	D87 Y88 K90 N91 F229 T232 R234 E271 M272 H273 R274 V286 G287 L289 R295 R300 R330 H331 T332 Y338 R339 T350 E390 G391	D59 Y60 K62 N63 F201 T204 R206 E243 M244 H245 R246 V258 G259 L261 R267 R272 R302 H303 T304 Y310 R311 T322 E362 G363
BS04	KIR	BZ	I93 L121 R124 Q125 V126 Y161 E162 E327 R385 F386 A387 T394 A397	I65 L93 R96 Q97 V98 Y133 E134 E299 R357 F358 A359 T366 A369
BS05	GDP	BZ	V20 D21 G23 K24 T25 T26 N136 K137 D139 M140 S174 L176	V18 D19 G21 K22 T23 T24 N108 K109 D111 M112 S146 L148

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005525 GTP binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4v8q, PDBe:4v8q, PDBj:4v8q
• PDBsum: 4v8q
• PubMed: 22422985
• UniProt: Q5SHN6|EFTU1_THET8 Elongation factor Tu-A (Gene Name=tufA)