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5tkm

Crystal structure of human APOBEC3B N-terminal Domain

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

DNA dC->dU-editing enzyme APOBEC-3B

Homo sapiens

UniProt Q9UH17

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ZINC ION × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ZINC ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2nbq 5cqd 5cqd 5cqh 5cqi 5cqk 5sxg 5sxg 5tkm 5tkm 6nfk 6nfl

13 assemblies; showing the first 12

Homodimer
5sxh 5sxh

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5td5 7rw6

2 assemblies

View Construct and Data Evidence
UniProt name ABC3B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–198； UniProt 1–191 Author chain B； PDBConstruct 8–198； UniProt 1–191

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_id5tkm
Deposition date deposition_date2016-10-07
Structure title titleCrystal structure of human APOBEC3B N-terminal Domain
Keywords keywordsHYDROLASE, DEAMINASE, APOBEC; HYDROLASE
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.

5tkm__assembly_1__model_1

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

Download this curve (.dat)

5tkm__assembly_1__model_1 | I(q)

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

5tkm__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）17.62 Å
Rg (electron density)16.18 Å
Total Rg17.32 Å
Atom count1567
Residues184
Excluded volume27746 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5tkm__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5tkm__assembly_2__model_1 monomeric （1） 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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5tkma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.97 — Cytidine deaminase-like
Superfamily Superfamily superfamilyc.97.1 — Cytidine deaminase-like
Family Family familyc.97.1.6 — apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains
Domain ID domain_idd5tkmb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.97 — Cytidine deaminase-like
Superfamily Superfamily superfamilyc.97.1 — Cytidine deaminase-like
Family Family familyc.97.1.6 — apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains
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7. Citations (1)