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2a57

Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine

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

6,7-dimethyl-8-ribityllumazine synthase

Schizosaccharomyces pombe

UniProt Q9UUB1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 5 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID × 5 PHOSPHATE ION × 5 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 10 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID × 10 PHOSPHATE ION × 10 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
1kyv 1kyv 1kyx 1kyx 1kyy 1kyy 1kz1 1kz1 1kz4 1kz4 1kz6 1kz6

19 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name RIB4_SCHPO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–159； UniProt 1–159 Author chain B； PDBConstruct 1–159； UniProt 1–159 Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain D； PDBConstruct 1–159； UniProt 1–159 Author chain E； PDBConstruct 1–159； UniProt 1–159

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_id2a57
Deposition date deposition_date2005-06-30
Structure title titleStructure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine
Keywords keywords6, 7-dimethyl-8-ribityllumazine synthase, riboflavin, riboflavin biosynthesis, LUSY, Transferase; TRANSFERASE
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.

2a57__assembly_1__model_1

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

Download this curve (.dat)

2a57__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.

2a57__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）27.22 Å
Rg (electron density)26.19 Å
Total Rg27.05 Å
Atom count5685
Residues730
Excluded volume101460 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2a57__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2a57__assembly_2__model_1 decameric （10） 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) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2a57a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.16 — Lumazine synthase
Superfamily Superfamily superfamilyc.16.1 — Lumazine synthase
Family Family familyc.16.1.1 — Lumazine synthase
Domain ID domain_idd2a57b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.16 — Lumazine synthase
Superfamily Superfamily superfamilyc.16.1 — Lumazine synthase
Family Family familyc.16.1.1 — Lumazine synthase
Domain ID domain_idd2a57c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.16 — Lumazine synthase
Superfamily Superfamily superfamilyc.16.1 — Lumazine synthase
Family Family familyc.16.1.1 — Lumazine synthase
Domain ID domain_idd2a57d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.16 — Lumazine synthase
Superfamily Superfamily superfamilyc.16.1 — Lumazine synthase
Family Family familyc.16.1.1 — Lumazine synthase
Domain ID domain_idd2a57e_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.16 — Lumazine synthase
Superfamily Superfamily superfamilyc.16.1 — Lumazine synthase
Family Family familyc.16.1.1 — Lumazine synthase

CATH v4.4 (5 domains)

Domain ID domain_id2a57A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id2a57B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id2a57C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id2a57D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id2a57E00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
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7. Citations (1)