Structure of PDB 5ak9 Chain A

Receptor sequence

>5ak9A (length=183)

ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAP
LMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMR
EQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLD
DHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP

3D structure

• PDB: 5ak9 Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.
• Chain: A
• Resolution: 2.601 Å

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

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	A	D21 T41 A42 K43 T76 R124 T150 H152 D154 H156 R157 N164 S166 L167	D17 T37 A38 K39 T72 R120 T146 H148 D150 H152 R153 N160 S162 L163	PDBbind-CN: Kd=0.3nM
BS02	dna	A	G20 D21 G22 Y25 Y29 K30 R33 R37 R77	G16 D17 G18 Y21 Y25 K26 R29 R33 R73	PDBbind-CN: Kd=0.3nM
BS03	dna	A	N32 R33 S34 E35 Y36 R37 S67 K68 Q70 D75 R81 S83 S84 K85 E117 G118 D119 M120 R126 W128 K130 D155 H158	N28 R29 S30 E31 Y32 R33 S63 K64 Q66 D71 R77 S79 S80 K81 E113 G114 D115 M116 R122 W124 K126 D151 H154	PDBbind-CN: Kd=0.3nM
BS04	MN	A	D21 A116	D17 A112
BS05	MN	A	G20 E117	G16 E113

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity

Biological Process

• GO:0006314 intron homing
• GO:0016539 intein-mediated protein splicing

External links

• PDB: RCSB:5ak9, PDBe:5ak9, PDBj:5ak9
• PDBsum: 5ak9
• PubMed: 26045557
• UniProt: P21505|DMO1_DESMO Homing endonuclease I-DmoI