Structure of PDB 5gad Chain i

Receptor sequence

>5gadi (length=450) Species: 562 (Escherichia coli)

NLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFIN
RVKEKAVGHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVV
LMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAE
QVGVDFFPSDVGQKPVDIVNAALKEAKLKFYDVLLVDTAGRLHVDEAMMD
EIKQVHASINPVETLFVVDAMTGQDAANTAKAFNEALPLTGVVLTKVDGD
ARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMPPPPPP
PPPPPPPPPPPPPPPPPPPPPPPPGFDLNDFLEQLRQMKNMGGPPPPPPP
PPPPPPPPPPPPPPPDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIA
AGCGMQVQDVNRLLKQFDDMQRMMKKMKKGGPPPPPPPPPPPPPPPPPPP

3D structure

• PDB: 5gad Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
• Chain: i
• Resolution: 3.7 Å

Enzymatic activity

• Enzyme Commision number: 3.6.5.4: signal-recognition-particle GTPase.

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	i	A378 N381 S382 M383 T384 M385 K386 R388 S397 R398 R401 G405 C406	A375 N378 S379 M380 T381 M382 K383 R385 S394 R395 R398 G402 C403
BS02	rna	i	K395 G396 N414 D422 R425 K432 X435 X449 X450 X451 X452 X453	K392 G393 N411 D419 R422 K429 X432 X446 X447 X448 X449 X450
BS03	peptide	i	X313 X317 Q337 M341 X354 Q419 M423 M426	X310 X314 Q334 M338 X351 Q416 M420 M423
BS04	GNP	i	Q109 G110 G112 K113 T114 T115 K119 R141 G193 K249 D251 G274 G276 E277	Q106 G107 G109 K110 T111 T112 K116 R138 G190 K246 D248 G271 G273 E274

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0008312 7S RNA binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0006612 protein targeting to membrane
• GO:0006614 SRP-dependent cotranslational protein targeting to membrane

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0048500 signal recognition particle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5gad, PDBe:5gad, PDBj:5gad
• PDBsum: 5gad
• PubMed: 26804923
• UniProt: P0AGD7|SRP54_ECOLI Signal recognition particle protein (Gene Name=ffh)