SAXSdb — 1ycd

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

Hypothetical 27.3 kDa protein in AAP1-SMF2 intergenic region

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-HYDROXY-4,5-DIOXOHEPTYL HYDROGEN PHOSPHONATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-HYDROXY-4,5-DIOXOHEPTYL HYDROGEN PHOSPHONATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHK9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 1–243 Author chain B； PDBConstruct 1–243； UniProt 1–243

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	1ycd
Deposition date deposition_date	2004-12-22
Structure title title	Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family
Keywords keywords	esterase, lipase, serine hydrolase, S. cerevisiae, Structural Genomics, Paris-Sud Yeast Structural Genomics, YSG, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1ycd__assembly_1__model_1

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

Download this curve (.dat)

1ycd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ycd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.83 Å
Rg (electron density)	17.43 Å
Total Rg	18.55 Å
Atom count	1895
Residues	237
Excluded volume	33961 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ycd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ycd__assembly_2__model_1`	monomeric （1）	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)

Entity 1 Entity 1 polymer

Description description	Hypothetical 27.3 kDa protein in AAP1-SMF2 intergenic region
Molecular weight formula_weight	27342.2 kDa
Mutation mutation	F109L
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	4732

MTVQIPKLLFLHGFLQNGKVFSEKSSGIRKLLKKANVQCDYIDAPVLLEKKDLPFEMDDEKWQATLDADVNRAWFYHSEISHELDISEGLKSVVDHIKANGPYDGIVGLSQGAALSSIITNKISELVPDHPQFKVSVVISGYSFTEPDPEHPGELRITEKFRDSFAVKPDMKTKMIFIYGASDQAVPSVRSKYLYDIYLKAQNGNKEKVLAYEHPGGHMVPNKKDIIRPIVEQITSSLQEASE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-HYDROXY-4,5-DIOXOHEPTYL HYDROGEN PHOSPHONATE
Molecular weight formula_weight	224.1 kDa
Mutation mutation	F109L
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	936

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1ycdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	1ycdB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	46.133 Å
Unit-cell length b length_b	53.329 Å
Unit-cell length c length_c	64.271 Å
Unit-cell angle α angle_alpha	102.85 °
Unit-cell angle β angle_beta	90.04 °
Unit-cell angle γ angle_gamma	112.47 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1675
R_work r_work	0.1656
R_free r_free	0.2022

Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family

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

Hypothetical 27.3 kDa protein in AAP1-SMF2 intergenic region

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

1ycd__assembly_1__model_1

1ycd__assembly_1__model_1 | I(q)

1ycd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family

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

Hypothetical 27.3 kDa protein in AAP1-SMF2 intergenic region

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

1ycd__assembly_1__model_1

1ycd__assembly_1__model_1 | I(q)

1ycd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)