Structure of PDB 5akn Chain A

Receptor sequence

>5aknA (length=178)

NVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPL
MQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMRE
QIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDD
HRHGVYVLNISLRDRIKFVHTILSSHLN

3D structure

• PDB: 5akn Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.
• Chain: A
• Resolution: 2.75 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 R157 S166 L167	D16 T36 A37 K38 T71 R119 T145 H147 D149 R152 S161 L162
BS02	dna	A	G20 D21 G22 Y25 Y29 K30 R33 R77	G15 D16 G17 Y20 Y24 K25 R28 R72
BS03	dna	A	N32 R33 S34 E35 Y36 R37 S67 K68 Q70 R81 S83 S84 K85 E117 W128 N129 K130 D155 H158	N27 R28 S29 E30 Y31 R32 S62 K63 Q65 R76 S78 S79 K80 E112 W123 N124 K125 D150 H153
BS04	dna	A	A116 D119 M120 R124 R126 W128	A111 D114 M115 R119 R121 W123
BS05	dna	A	R104 H175 H181	R99 H170 H176
BS06	MN	A	D21 A116	D16 A111
BS07	MN	A	G20 E117	G15 E112

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity

Biological Process

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

External links

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