5y1y

Complex structure of nitroxoline with the first bromodomain of BRD4

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

Bromodomain-containing protein 4

Homo sapiens

UniProt O60885

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 5-nitroquinolin-8-ol × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name BRD4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–125; UniProt 44–167

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_id5y1y
Deposition date deposition_date2017-07-21
Structure title titleComplex structure of nitroxoline with the first bromodomain of BRD4
Keywords keywordsBRD4 inhibitor Approved drugs, TRANSCRIPTION; TRANSCRIPTION
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.

5y1y__assembly_1__model_1

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

Download this curve (.dat)

5y1y__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.

5y1y__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)15.80 Å
Rg (electron density)14.70 Å
Total Rg15.87 Å
Atom count1051
Residues124
Excluded volume18916 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5y1y__assembly_1__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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5y1ya1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd5y1ya2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id5y1yA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
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7. Citations (1)