Structure of PDB 5akm Chain A

Receptor sequence

>5akmA (length=183)

ENVSGISAYLLGLIISDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAP
LMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMR
EQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLD
DHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP

3D structure

• PDB: 5akm Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.
• Chain: A
• Resolution: 2.4 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 K43 T76 R77 R124 T150 H152 D154 R157 S166 L167	D17 T37 K39 T72 R73 R120 T146 H148 D150 R153 S162 L163
BS02	dna	A	S20 G22 Y25 Y29 K30 R33 R37 R77	S16 G18 Y21 Y25 K26 R29 R33 R73
BS03	dna	A	N32 R33 S34 E35 Y36 R37 S67 K68 Q70 R81 S83 S84 K85 E117 W128 K130 D155 H158	N28 R29 S30 E31 Y32 R33 S63 K64 Q66 R77 S79 S80 K81 E113 W124 K126 D151 H154
BS04	dna	A	A116 D119 K120 R126 W128	A112 D115 K116 R122 W124
BS05	dna	A	K86 Y89 N93 R97	K82 Y85 N89 R93
BS06	MG	A	D21 A116	D17 A112

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity

Biological Process

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

External links

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