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5akn

THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HOMING ENDONUCLEASE I-DMOI

DESULFUROCOCCUS MOBILIS

UniProt P21505

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 4 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' × 1 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3 × 1 D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' × 1 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' × 1 MANGANESE (II) ION × 2 water × 5 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' × 1 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' × 1 ;5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' ; × 1 MANGANESE (II) ION × 2 water × 4 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' × 1 ;5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' ; × 1 ;5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3' ; × 1 MANGANESE (II) ION × 2 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1b24

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2vs7 2vs7 2vs7 2vs8 2vs8 2vs8 4d6n 4d6n 4d6n 4d6o 4d6o 4d6o

54 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DMO1_DESMO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–188； UniProt 2–188 Author chain F； PDBConstruct 2–188； UniProt 2–188 Author chain K； PDBConstruct 2–188； UniProt 2–188

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id5akn
Deposition date deposition_date2015-03-04
Structure title titleTHE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN
Keywords keywordsHYDROLASE-DNA COMPLEX, HYDROLASE, GENE TARGETING, GENETICS, PROTEIN-DNA INTERACTION, HOMING ENDONUCLEASES; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5akn__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5akn__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5akn__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）23.02 Å
Rg (electron density)21.43 Å
Total Rg22.27 Å
Atom count2541
Residues234
Excluded volume42303 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5akn__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5akn__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5akn__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5aknA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id5aknA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id5aknF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id5aknF02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id5aknK01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id5aknK02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
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7. Citations (1)