Structure of PDB 5ybi Chain A

Receptor sequence

>5ybiA (length=337) Species: 623 (Shigella flexneri)

SHMHTQVGRGLLGAVVNPLGEVTDKFAVTDNSEILYRPVDNAPPLYSERA
AIEKPFLTGIKVIDSLLTCGEGQRMGIFASAGCGKTFLMNMLIEHSGADI
YVIGLIGERGREVTETVDYLKNSEKKSRCVLVYATSDYSSVDRCNAAYIA
TAIAEFFRTEGHKVALFIDSLTRYARALRDVALAAGESPARRGYPVSVFD
SLPRLLERPGKLKAGGSITAFYTVLLEDDDFDPLAEEVRSILDGHIYLSR
NLAQKGQFPAIDSLKSISRVFTQVVDEKHRIMAAAFRELLSEIEELRTIS
QDKIYNKISVVESFLKQDYRLGFTYEQTMELIGETIR

3D structure

• PDB: 5ybi Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri.
• Chain: A
• Resolution: 2.268 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K165 E188 R189 R350
• Catalytic site (residue number reindexed from 1): K85 E108 R109 R269
• Enzyme Commision number: 7.4.2.8: protein-secreting ATPase.

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	ANP	A	G162 G164 K165 T166 F167 F339 Y412	G82 G84 K85 T86 F87 F258 Y319	PDBbind-CN: -logKd/Ki=3.49,Kd=322.48uM
BS02	MG	A	G290 K291	G210 K211
BS03	MG	A	M171 P340	M91 P259
BS04	MG	A	T417 Y418	T324 Y325
BS05	MG	A	Q86 G100	Q6 G20
BS06	MG	A	L146 R368	L66 R287
BS07	MG	A	R189 R191	R109 R111
BS08	MG	A	V87 G88 I233 F236 F237	V7 G8 I153 F156 F157

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0009058 biosynthetic process
• GO:0030254 protein secretion by the type III secretion system

Cellular Component

• GO:0005737 cytoplasm
• GO:0030257 type III protein secretion system complex

External links

• PDB: RCSB:5ybi, PDBe:5ybi, PDBj:5ybi
• PDBsum: 5ybi
• PubMed: 30013545
• UniProt: P0A1C1|SCTN_SHIFL Type 3 secretion system ATPase (Gene Name=sctN)