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2d5v

Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter

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

Hepatocyte nuclear factor 6

Rattus norvegicus

UniProt P70512

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*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' × 1 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' × 1 ACETATE ION × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' × 1 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' × 1 ACETATE ION × 1 GLYCEROL × 2 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2d5v 2d5v

2 assemblies

View Construct and Data Evidence
UniProt name HNF6_RAT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–156； UniProt 289–444 Author chain B； PDBConstruct 1–156； UniProt 289–444

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_id2d5v
Deposition date deposition_date2005-11-07
Structure title titleCrystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter
Keywords keywordsTranscription factor, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/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.

2d5v__assembly_2__model_1

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

Download this curve (.dat)

2d5v__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.

2d5v__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）18.36 Å
Rg (electron density)18.35 Å
Total Rg19.05 Å
Atom count1673
Residues161
Excluded volume28341 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2d5v__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2d5v__assembly_2__model_1 trimeric （3） 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 (6)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2d5va1
Class classa — All alpha proteins
Fold Fold folda.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamilya.35.1 — lambda repressor-like DNA-binding domains
Family Family familya.35.1.7 — CUT domain
Domain ID domain_idd2d5va2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.0 — automated matches
Domain ID domain_idd2d5vb1
Class classa — All alpha proteins
Fold Fold folda.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamilya.35.1 — lambda repressor-like DNA-binding domains
Family Family familya.35.1.7 — CUT domain
Domain ID domain_idd2d5vb2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id2d5vA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily40 — lambda repressor-like DNA-binding domains
Domain ID domain_id2d5vA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id2d5vB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily40 — lambda repressor-like DNA-binding domains
Domain ID domain_id2d5vB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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7. Citations (1)