← Back to search
4nih

Crystal structure of AlkB E136L mutant protein with cofactors bound to dsDNA containing m6A/A

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-ketoglutarate-dependent dioxygenase AlkB

Escherichia coli

UniProt P05050

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3' × 1 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3' × 1 MANGANESE (II) ION × 1 2-OXOGLUTARIC ACID × 1 GLYCEROL × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2fdj 3i3q 3i3q 3khb 3khb 3t3y 3t4h 3t4v 4jht 4rfr 6y0q 6ypv

13 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2fd8 2fdf 2fdg 2fdh 2fdi 2fdk 3bi3 3bie 3bkz 3i2o 3i3m 3i49

26 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ALKB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–205； UniProt 12–216

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4nih
Deposition date deposition_date2013-11-06
Structure title titleCrystal structure of AlkB E136L mutant protein with cofactors bound to dsDNA containing m6A/A
Keywords keywordsDNA/RNA direct repair, jelly-roll fold, DNA/RNA demethylation repair, Fe(II), 2-KG, OXIDOREDUCTASE-DNA complex; OXIDOREDUCTASE/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

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.

4nih__assembly_1__model_1

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

Download this curve (.dat)

4nih__assembly_1__model_1 | I(q)

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

4nih__assembly_1__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）19.31 Å
Rg (electron density)18.06 Å
Total Rg19.00 Å
Atom count2093
Residues224
Excluded volume35628 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4nih__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4niha_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.2 — Clavaminate synthase-like
Family Family familyb.82.2.10 — AlkB-like

CATH v4.4 (1 domains)

Domain ID domain_id4nihA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily590 — Alpha-ketoglutarate-dependent dioxygenase AlkB-like
▶

7. Citations (1)