Structure of PDB 5gaf Chain i

Receptor sequence

>5gafi (length=398) Species: 562 (Escherichia coli)

MFDNLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVRE
FINRVKEKAVGHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPP
AVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLET
LAEQVGVDFFPSDVGQKPVDIVNAALKEAKLKFYDVLLVDTAGRLHVDEA
MMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNEALPLTGVVLTKV
DGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMGFD
LNDFLEQLRQMKNDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAG
CGMQVQDVNRLLKQFDDMQRMMKKMKKGGPPPPPPPPPPPPPPPPPPP

3D structure

• PDB: 5gaf Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon
• Chain: i
• Resolution: 4.3 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	A323 N326 S327 M328 T329 M330 K331 R333 S342 R343 R346 G350 C351
BS02	rna	i	K395 G396 K399 Q411 N414 D421 R425 K429 X435 X450 X451 X452 X453	K340 G341 K344 Q356 N359 D366 R370 K374 X380 X395 X396 X397 X398
BS03	peptide	i	Q337 M341 Q419 M423 M427	Q307 M311 Q364 M368 M372
BS04	GNP	i	Q109 G110 G112 K113 T114 T115 Q147 K249 D251 G274 G276 E277	Q109 G110 G112 K113 T114 T115 Q147 K249 D251 G274 G276 E277

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005525 GTP binding
• GO:0008312 7S RNA binding
• GO:0016887 ATP hydrolysis activity

Biological Process

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

Cellular Component

• GO:0048500 signal recognition particle

External links

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