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1kb2

Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element

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

Vitamin D3 Receptor

Homo sapiens

UniProt P11473

State in the Current Structure

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

Other States of the Same Protein in the Database

Monomer
1db1 1ie8 1ie9 1s0z 1s19 1txi 2ham 2har 2has 2hb7 2hb8 3a2i

48 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1kb2 1kb4 1kb6 1ynw

4 assemblies

View Construct and Data Evidence
UniProt name VDR_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–110； UniProt 16–125 Author chain B； PDBConstruct 1–110； UniProt 16–125

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_id1kb2
Deposition date deposition_date2001-11-05
Structure title titleCrystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element
Keywords keywordsVDR, NUCLEAR RECEPTOR, PROTEIN-DNA COMPLEX, VITAMIN D, 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.

1kb2__assembly_1__model_1

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

Download this curve (.dat)

1kb2__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.

1kb2__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）21.66 Å
Rg (electron density)21.41 Å
Total Rg22.04 Å
Atom count2100
Residues210
Excluded volume34943 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1kb2__assembly_1__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 (5)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1kb2a_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor
Domain ID domain_idd1kb2b_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor

CATH v4.4 (2 domains)

Domain ID domain_id1kb2A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id1kb2B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
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7. Citations (1)