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4zq9

X-ray structure of AAV-2 OBD bound to AAVS1 site 3:1

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

Protein Rep68

Adeno-associated virus 2 (isolate Srivastava/1982)

UniProt P03132

State in the Current Structure

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

Other States of the Same Protein in the Database

Monomer
1u0j 4zo0 4zo0 4zo0 5dcx 5dcx 5dcx 5dcx 5dcx 5dcx 5dcx 5dcx

15 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4zq9 6xb8 6xb8 7jse 7jsf 7jsg 7jsh 7jsi 9bc5 9bu7 9rwg

11 assemblies

View Construct and Data Evidence
UniProt name REP68_AAV2S
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–211； UniProt 1–208 Author chain B； PDBConstruct 4–211； UniProt 1–208 Author chain C； PDBConstruct 4–211； UniProt 1–208

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_id4zq9
Deposition date deposition_date2015-05-08
Structure title titleX-ray structure of AAV-2 OBD bound to AAVS1 site 3:1
Keywords keywordsDNA binding protein, Adeno-Associated Virus, Nuclease, origin-binding protein, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

4zq9__assembly_1__model_1

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

Download this curve (.dat)

4zq9__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4zq9__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）32.72 Å
Rg (electron density)33.12 Å
Total Rg33.37 Å
Atom count5438
Residues603
Excluded volume94494 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4zq9__assembly_1__model_1 pentameric （5） 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 (5)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4zq9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4zq9B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4zq9C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily20 —
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7. Citations (1)