SAXSdb — 3syx

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

Sprouty-related, EVH1 domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	YTTRIUM (III) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPRE1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–130； UniProt 13–131

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	3syx
Deposition date deposition_date	2011-07-18
Structure title title	Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.
Keywords keywords	;WH1 domain, Human sprouty-related, EVH1 domain-containing protein, Q7Z699, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, PSI-Biology, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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.

3syx__assembly_1__model_1

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

Download this curve (.dat)

3syx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3syx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.85 Å
Rg (electron density)	14.33 Å
Total Rg	15.63 Å
Atom count	934
Residues	118
Excluded volume	16601 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3syx__assembly_1__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	Sprouty-related, EVH1 domain-containing protein 1
Molecular weight formula_weight	14830.0 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	955

MGHHHHHHSHMSYARVRAVVMTRDDSSGGWLPLGGSGLSSVTVFKVPHQEENGCADFFIRGERLRDKMVVLECMLKKDLIYNKVTPTFHHWKIDDKKFGLTFQSPADARAFDRGIRRAIEDISQGCPESK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	YTTRIUM (III) ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3syxa1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.4 — Enabled/VASP homology 1 domain (EVH1 domain)

Domain ID domain_id	d3syxa2
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

CATH v4.4 (1 domains)

Domain ID domain_id	3syxA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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Unit-cell length a length_a	52.754 Å
Unit-cell length b length_b	52.754 Å
Unit-cell length c length_c	121.638 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.453 Å
Low-resolution limit resolution_low	26.377 Å
R factor r_factor	0.2300
R_work r_work	0.2280
R_free r_free	0.2710

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.

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

Sprouty-related, EVH1 domain-containing protein 1

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

3syx__assembly_1__model_1

3syx__assembly_1__model_1 | I(q)

3syx__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.

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

Sprouty-related, EVH1 domain-containing protein 1

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

3syx__assembly_1__model_1

3syx__assembly_1__model_1 | I(q)

3syx__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)