Structure of PDB 6eko Chain B

Receptor sequence

>6ekoB (length=312) Species: 294 (Pseudomonas fluorescens)

MQKYRLYEKDGSPVQDFNRFVKGWLDIEFGLKEHQPPKVFDTIRDKYNEA
IEAVVLSGVAPRTAHKAALSTLTELLFGHDLAKELSARLDIQPIGVGGFR
SAHSQAFAKNVGENFVNLMVYALACILKDNDDVLVDKGLPPHLKKALTLS
RECRIKDTLREIKIPIEGDLCVFSRSNHMNAIVISAATRLKEVFHIGTMW
ALFSDVAKDEYCLNKWGLKVESSESLKDTMYVFATADMINKDGARSQGCD
VERETPRNLIAMDASFFDYVFVSKMGIGHVSSDLSLKYGRESLFHELGCI
IDMIEQKFDILL

3D structure

• PDB: 6eko Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.
• Chain: B
• Resolution: 2.284 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.4: type II site-specific deoxyribonuclease.

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	dna	B	H34 Q35 K38 R88 I94 G98 F99 R100 Q105 A106 K109 N110 E192 H195 R253 R257 N258 L259	H34 Q35 K38 R88 I94 G98 F99 R100 Q105 A106 K109 N110 E192 H195 R253 R257 N258 L259
BS02	dna	B	L76 F77 H79 F107 A108 K109 G112 E167 D169 A187 T188 R189 K191 R245 S246 Q247	L76 F77 H79 F107 A108 K109 G112 E167 D169 A187 T188 R189 K191 R245 S246 Q247
BS03	CA	B	D169 A186	D169 A186

Gene Ontology

Molecular Function

• GO:0009036 type II site-specific deoxyribonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006259 DNA metabolic process

External links

• PDB: RCSB:6eko, PDBe:6eko, PDBj:6eko
• PDBsum: 6eko
• PubMed: 30445642
• UniProt: A0A452CST9