Structure of PDB 5ybh Chain B

Receptor sequence

>5ybhB (length=340) Species: 623 (Shigella flexneri)

GSHMHTQVGRGLLGAVVNPLGEVTDKFAVTDNSEILYRPVDNAPPLYSER
AAIEKPFLTGIKVIDSLLTCGEGQRMGIFASAGCGKTFLMNMLIEHSGAD
IYVIGLIGERGREVTETVDYLKNSEKKSRCVLVYATSDYSSVDRCNAAYI
ATAIAEFFRTEGHKVALFIDSLTRYARALRDVALAAGESPARRGYPVSVF
DSLPRLLERPGKLKAGGSITAFYTVLLEDDDFADPLAEEVRSILDGHIYL
SRNLAQKGQFPAIDSLKSISRVFTQVVDEKHRIMAAAFRELLSEIEELRT
IISQDKIYNKISVVESFLKQDYRLGFTYEQTMELIGETIR

3D structure

• PDB: 5ybh Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri
• Chain: B
• Resolution: 2.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K165 E188 R189 R350
• Catalytic site (residue number reindexed from 1): K86 E109 R110 R271
• 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	MG	B	G177 A178 Y181 K205	G98 A99 Y102 K126
BS02	MG	B	I186 S250 R253	I107 S171 R174
BS03	MG	B	G162 C163 K165	G83 C84 K86
BS04	MG	B	D144 T148 C149	D65 T69 C70
BS05	MG	B	R320 G325 R350	R241 G246 R271
BS06	MG	B	E188 E192	E109 E113
BS07	MG	B	P283 E318	P204 E239

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