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2pe5

Crystal Structure of the Lac Repressor bound to ONPG in repressed state

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

Lactose operon repressor

Escherichia coli

UniProt P03023

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 ;DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3') ; × 2 2-nitrophenyl beta-D-galactopyranoside × 2 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3') ; × 2 2-nitrophenyl beta-D-galactopyranoside × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1efa 1lqc

2 assemblies

Homodimer
1jwl 1jye 1jyf 2p9h 2paf

5 assemblies

Homotetramer
1lbh 1lbi 1tlf 3edc

4 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1cjg 1efa 1jwl 1l1m 1lbg 1lbg 1lcc 1lcd 1osl 2bjc 2kei 2kej

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name LACI_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–330； UniProt 2–331 Author chain B； PDBConstruct 1–330； UniProt 2–331 Author chain C； PDBConstruct 1–330； UniProt 2–331

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_id2pe5
Deposition date deposition_date2007-04-02
Structure title titleCrystal Structure of the Lac Repressor bound to ONPG in repressed state
Keywords keywords;Lac repressor, allosteric effectors, gene regulation, DNA-binding, Transcription, Transcription regulation, 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.

2pe5__assembly_2__model_1

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

Download this curve (.dat)

2pe5__assembly_2__model_1 | I(q)

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

2pe5__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）31.29 Å
Rg (electron density)29.88 Å
Total Rg30.55 Å
Atom count5676
Residues690
Excluded volume98949 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2pe5__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2pe5__assembly_2__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 (3)

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2pe5a1
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.35.1.5 — GalR/LacI-like bacterial regulator
Domain ID domain_idd2pe5a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd2pe5b1
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.35.1.5 — GalR/LacI-like bacterial regulator
Domain ID domain_idd2pe5b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd2pe5c1
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.35.1.5 — GalR/LacI-like bacterial regulator
Domain ID domain_idd2pe5c2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (9 domains)

Domain ID domain_id2pe5A01
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_id2pe5A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pe5A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pe5B01
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_id2pe5B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pe5B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pe5C01
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_id2pe5C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2pe5C03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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7. Citations (1)