SAXSdb — 1kyy

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

6,7-Dimethyl-8-ribityllumazine Synthase

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	PHOSPHATE ION × 5 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 5 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 10	PHOSPHATE ION × 10 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

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_id	1kyy
Deposition date deposition_date	2002-02-06
Structure title title	Lumazine Synthase from S.pombe bound to nitropyrimidinedione
Keywords keywords	riboflavin biosynthesis, lumazine synthase, Schizosaccharomyces pombe, ligand binding, TRANSFERASE; TRANSFERASE
Experimental Method method	X-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.

1kyy__assembly_2__model_1

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

Download this curve (.dat)

1kyy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kyy__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.23 Å
Rg (electron density)	33.46 Å
Total Rg	34.12 Å
Atom count	11578
Residues	1488
Excluded volume	206110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kyy__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kyy__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 (4)

Entity 1 Entity 1 polymer

Description description	6,7-Dimethyl-8-ribityllumazine Synthase
Molecular weight formula_weight	17206.8 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	5966

MFSGIKGPNPSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKALY

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
Molecular weight formula_weight	306.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1kyya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1kyyb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1kyyc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1kyyd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1kyye_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

CATH v4.4 (5 domains)

Domain ID domain_id	1kyyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1kyyB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1kyyC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1kyyD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	1kyyE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

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Unit-cell length a length_a	111.261 Å
Unit-cell length b length_b	145.044 Å
Unit-cell length c length_c	127.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	15.579 Å
R factor r_factor	0.1860
R_work r_work	0.1830
R_free r_free	0.2058

Lumazine Synthase from S.pombe bound to nitropyrimidinedione

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

6,7-Dimethyl-8-ribityllumazine Synthase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1kyy__assembly_2__model_1

1kyy__assembly_2__model_1 | I(q)

1kyy__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Lumazine Synthase from S.pombe bound to nitropyrimidinedione

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

6,7-Dimethyl-8-ribityllumazine Synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1kyy__assembly_2__model_1

1kyy__assembly_2__model_1 | I(q)

1kyy__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)