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1ep3

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.

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

DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)

Lactococcus lactis

UniProt P54322

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT) × 2 （P56968） FLAVIN MONONUCLEOTIDE × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ep1 1ep2 1ep3

3 assemblies

View Construct and Data Evidence
UniProt name PYRDB_LACLC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–311； UniProt 1–311

DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)

Lactococcus lactis

UniProt P56968

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT) × 2 （P54322） FLAVIN MONONUCLEOTIDE × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ep1 1ep2 1ep3

3 assemblies

View Construct and Data Evidence
UniProt name PYRK_LACLC
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–262； UniProt 1–262

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_id1ep3
Deposition date deposition_date2000-03-27
Structure title titleCRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.
Keywords keywordsHeterotetramer, ALPHA-BETA barrel, BETA sandwich, FAD domain, ALPHA/BETA NADP domain, FeS cluster binding domain, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1ep3__assembly_1__model_1

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

Download this curve (.dat)

1ep3__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.

1ep3__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）32.47 Å
Rg (electron density)31.78 Å
Total Rg32.25 Å
Atom count8776
Residues1144
Excluded volume158070 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ep3__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 (6)

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1ep3a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.4 — FMN-linked oxidoreductases
Family Family familyc.1.4.1 — FMN-linked oxidoreductases
Domain ID domain_idd1ep3b1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.2 — Ferredoxin reductase FAD-binding domain-like
Domain ID domain_idd1ep3b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.3 — Dihydroorotate dehydrogenase B, PyrK subunit

CATH v4.4 (4 domains)

Domain ID domain_id1ep3A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1ep3B01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1ep3B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
Domain ID domain_id1ep3B03
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology240 — Dihydroorotate dehydrogenase B (pyrk subunit); domain 3
Homologous superfamily homologous superfamily10 — Dihydroorotate dehydrogenase, electron transfer subunit
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7. Citations (4)