SAXSdb — 1mqs

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

Sly1 Protein

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Integral Membrane Protein SED5 × 1 （Q01590） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Integral Membrane Protein SED5 × 2 （Q01590） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SLY1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–671； UniProt 1–666

Integral Membrane Protein SED5

Saccharomyces cerevisiae

UniProt Q01590

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Sly1 Protein × 1 （P22213） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Sly1 Protein × 2 （P22213） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SED5_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–50； UniProt 1–45

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	1mqs
Deposition date deposition_date	2002-09-17
Structure title title	Crystal structure of Sly1p in complex with an N-terminal peptide of Sed5p
Keywords keywords	SM-protein, SNARE, syntaxin, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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.

1mqs__assembly_2__model_1

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

Download this curve (.dat)

1mqs__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mqs__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.45 Å
Rg (electron density)	36.72 Å
Total Rg	37.09 Å
Atom count	9410
Residues	1208
Excluded volume	168070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mqs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mqs__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Sly1 Protein
Molecular weight formula_weight	75655.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4725

GKSASMAVEEIASRKDISLRDMQISAILKMLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVPAIYFVSPTKENIDIIVNDLKSDKYSEFYINFTSSLPRNLLEDLAQQVSITGKSDKIKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNSSSTSTLQGNDSLERGVLIILDRNIDFASMFSHSWIYQCMVFDIFKLSRNTVTIPLESKENGTDNTTAKPLATKKYDIEPNDFFWMENSHLPFPEAAENVEAALNTYKEEAAEITRKTGVTNISDLDPNSNNDTVQIQEVVKKLPELTAKKNTIDTHMNIFAALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDGKTNNLEDKLRSFIVLYLTSTTGLPKDFVQNVENYFKENDYDINALKYVYKLREFMQLSNMSLQNKSLEDGSDSAFKPSNLTLSGIYGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAIMDPLNSSQKNLETTDSYLYIDPKITRGSHTRKPKRQSYNKSLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVMYGSTAITTPAEFLNEISRLGASNSSNNDA

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 polymer

Description description	Integral Membrane Protein SED5
Molecular weight formula_weight	5949.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GAMAGMNIKDRTSEFQQSVLSYKKRNKNFREQQRERLQEKESENFANNTT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1mqsa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.25 — Sec1/munc18-like (SM) proteins
Superfamily Superfamily superfamily	e.25.1 — Sec1/munc18-like (SM) proteins
Family Family family	e.25.1.1 — Sec1/munc18-like (SM) proteins

CATH v4.4 (4 domains)

Domain ID domain_id	1mqsA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2060 — Sec1/Munc18 (SM) protein, domain 1

Domain ID domain_id	1mqsA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1910 — Sec1/Munc18 (SM) protein, domain 2

Domain ID domain_id	1mqsA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

Domain ID domain_id	1mqsA04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	161.056 Å
Unit-cell length b length_b	161.056 Å
Unit-cell length c length_c	88.209 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2573
R_free r_free	0.2904

Crystal structure of Sly1p in complex with an N-terminal peptide of Sed5p

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

Sly1 Protein

State in the Current Structure

Other States of the Same Protein in the Database

Integral Membrane Protein SED5

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

1mqs__assembly_2__model_1

1mqs__assembly_2__model_1 | I(q)

1mqs__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (4)

Crystal structure of Sly1p in complex with an N-terminal peptide of Sed5p

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

Sly1 Protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Integral Membrane Protein SED5

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

1mqs__assembly_2__model_1

1mqs__assembly_2__model_1 | I(q)

1mqs__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (4)