SAXSdb — 2y5s

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

DIHYDROPTEROATE SYNTHASE

BURKHOLDERIA CENOCEPACIA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	7,8-DIHYDROPTEROATE × 2 CHLORIDE ION × 2 1,2-ETHANEDIOL × 16 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B4E5F5_BURCJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–294； UniProt 1–292 Author chain B； PDBConstruct 3–294； UniProt 1–292

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	2y5s
Deposition date deposition_date	2011-01-17
Structure title title	Crystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.
Keywords keywords	TRANSFERASE, FOLATE BIOSYNTHESIS; 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.

2y5s__assembly_1__model_1

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

Download this curve (.dat)

2y5s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y5s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.02 Å
Rg (electron density)	26.24 Å
Total Rg	26.90 Å
Atom count	4254
Residues	561
Excluded volume	75721 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y5s__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	DIHYDROPTEROATE SYNTHASE
Molecular weight formula_weight	31002.5 kDa
EC 编号 ec_number	2.5.1.15
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4665

GHMSTFLPAPLQCGRFELTFERPLVMGILNATPDSFSDGGRFLARDDALRRAERMIAEGADLLDIGGESTRPGAPPVPLDEELARVIPLVEALRPLNVPLSIDTYKPAVMRAALAAGADLINDIWGFRQPGAIDAVRDGNSGLCAMHMLGEPQTMQVGEPDYGDVVTDVRDFLAARAQALRDAGVAAERICVDPGFGFGKAVVDDNYALLAALPDTAPARPDGRAYPILAGMSRKSMLGAVIGGKPPLERVAASVAAALCAVERGAAIVRVHDVAATVDALSVWNAVRAAARQR

Source Source

Source organism organism	BURKHOLDERIA CENOCEPACIA
NCBI taxonomy ID ncbi_taxonomy_id	95486
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	7,8-DIHYDROPTEROATE
Molecular weight formula_weight	314.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	305

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2y5sa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.0 — automated matches

Domain ID domain_id	d2y5sa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2y5sb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2y5sA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	2y5sB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

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Unit-cell length a length_a	73.662 Å
Unit-cell length b length_b	86.920 Å
Unit-cell length c length_c	88.795 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	62.110 Å
R factor r_factor	0.1774
R_work r_work	0.1756
R_free r_free	0.2111

Crystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.

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

DIHYDROPTEROATE 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

2y5s__assembly_1__model_1

2y5s__assembly_1__model_1 | I(q)

2y5s__assembly_1__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.

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

DIHYDROPTEROATE 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

2y5s__assembly_1__model_1

2y5s__assembly_1__model_1 | I(q)

2y5s__assembly_1__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)