← Back to search
1nqv

Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-nitroso-6-ribityl-amino-2,4(1H,3H)pyrimidinedione

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

6,7-dimethyl-8-ribityllumazine synthase

Aquifex aeolicus

UniProt O66529

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 60 PHOSPHATE ION × 60 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 60 water × 60 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8yt4 8yt4

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1hqk 1nqu 1nqv 1nqw 1nqx 28ro 5mpp 5mq3 5mq7 7x7m 8f25 8pvj

31 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
7a4f 7a4g 7a4h 7a4i 7a4j 9ryj 9ryk 9rym

8 assemblies

View Construct and Data Evidence
UniProt name RISB_AQUAE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–154； UniProt 1–154 Author chain B； PDBConstruct 1–154； UniProt 1–154 Author chain C； PDBConstruct 1–154； UniProt 1–154 Author chain D； PDBConstruct 1–154； UniProt 1–154 Author chain E； PDBConstruct 1–154； UniProt 1–154

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1nqv
Deposition date deposition_date2003-01-23
Structure title titleCrystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-nitroso-6-ribityl-amino-2,4(1H,3H)pyrimidinedione
Keywords keywordsLumazine synthase, Aquifex aeolicus, inhibitor complex, vitamin biosynthesis, catalytic mechanism, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

1nqv__assembly_1__model_1

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

Download this curve (.dat)

1nqv__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1nqv__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）63.89 Å
Rg (electron density)62.86 Å
Total Rg63.16 Å
Atom count72120
Residues9240
Excluded volume1282900 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1nqv__assembly_1__model_1 60-meric （60） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1nqva_
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_idd1nqvb_
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_idd1nqvc_
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_idd1nqvd_
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_idd1nqve_
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_id1nqvA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id1nqvB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id1nqvC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id1nqvD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
Domain ID domain_id1nqvE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily960 — Lumazine/riboflavin synthase
▶

7. Citations (1)