SAXSdb — 5dbe

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

Cysteine synthase

Haemophilus influenzae KW20

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	C-terminal peptide from Serine acetyltransferase × 2 （P29847） GLYCEROL × 4 O-ACETYLSERINE × 2 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYSK_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 17–332； UniProt 1–316

C-terminal peptide from Serine acetyltransferase

OrganismNot specified

UniProt P29847

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cysteine synthase × 2 （P45040） GLYCEROL × 4 O-ACETYLSERINE × 2 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYSE_SALTY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–10； UniProt 264–273

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	5dbe
Deposition date deposition_date	2015-08-21
Structure title title	Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A
Keywords keywords	;AMINO-ACID BIOSYNTHESIS, CYSTEINE BIOSYNTHESIS, TRANSFERASE, PYRIDOXAL PHOSPHATE, TRANSFERASE-TRANSFERASE INHIBITOR COMP, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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.

5dbe__assembly_1__model_1

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

Download this curve (.dat)

5dbe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dbe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.82 Å
Rg (electron density)	23.83 Å
Total Rg	24.65 Å
Atom count	4608
Residues	624
Excluded volume	81978 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dbe__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)

Entity 1 Entity 1 polymer

Description description	Cysteine synthase
Molecular weight formula_weight	35232.3 kDa
EC 编号 ec_number	2.5.1.47
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	2348

HHHHHHSSGLVPRGSHMAIYADNSYSIGNTPLVRLKHFGHNGNVVVKIEGRNPSYSVKCRIGANMVWQAEKDGTLTKGKEIVDATSGNTGIALAYVAAARGYKITLTMPETMSLERKRLLCGLGVNLVLTEGAKGMKGAIAKAEEIVASDPSRYVMLKQFENPANPQIHRETTGPEIWKDTDGKVDVVVAGVGTGGSITGISRAIKLDFGKQITSVAVEPVESPVISQTLAGEEVKPGPHKIQGIGAGFIPKNLDLSIIDRVETVDSDTALATARRLMAEEGILAGISSGAAVAAADRLAKLPEFADKLIVVILPSASERYLSTALFEGIEG

Source Source

Source organism organism	Haemophilus influenzae KW20
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	C-terminal peptide from Serine acetyltransferase
Molecular weight formula_weight	1177.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

HHTFEYGDGI

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	O-ACETYLSERINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
Molecular weight formula_weight	316.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5dbeX01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dbeX02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

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Unit-cell length a length_a	112.643 Å
Unit-cell length b length_b	112.643 Å
Unit-cell length c length_c	45.898 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.1848
R_work r_work	0.1825
R_free r_free	0.2272

Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A

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

Cysteine synthase

State in the Current Structure

Other States of the Same Protein in the Database

C-terminal peptide from Serine acetyltransferase

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

5dbe__assembly_1__model_1

5dbe__assembly_1__model_1 | I(q)

5dbe__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A

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

Cysteine 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

C-terminal peptide from Serine acetyltransferase

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

5dbe__assembly_1__model_1

5dbe__assembly_1__model_1 | I(q)

5dbe__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)