SAXSdb — 1ddv

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

GLGF-DOMAIN PROTEIN HOMER

Rattus norvegicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 4–114	Fragment：HOMER EVH1 RESIDUES 1-111	METABOTROPIC GLUTAMATE RECEPTOR MGLUR5 × 1 （P31424）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 4–114	Fragment：HOMER EVH1 RESIDUES 1-111	METABOTROPIC GLUTAMATE RECEPTOR MGLUR5 × 2 （P31424）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1DDV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DDW HOMER EVH1 DOMAIN UNLIGANDED Deposited 1999-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–123（120 aa） Fragment：HOMER EVH1 DOMAIN RESIDUES 1-120	Mutation：NONE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, Magnesium sulfate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.285
1I2H CRYSTAL STRUCTURE ANALYSIS OF PSD-ZIP45(HOMER1C/VESL-1L)CONSERVED HOMER 1 DOMAIN Deposited 2001-02-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–163（163 aa） Fragment：N-TERMINAL CONSERVED HOMER 1 REGION (CH1 DOMAIN)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.218
3CVE Crystal Structure of the carboxy terminus of Homer1 Deposited 2008-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366 Chain B 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366 Chain C 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366 Chain D 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366	Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6；297 K；0.1 M MES, 0.1 M ammonium sulfate, 16% PEG1000, 10% glycerol, pH 6.0, hanging drop, temperature 297K	Resolution 1.75 Å R-free 0.289
3CVE Crystal Structure of the carboxy terminus of Homer1 Deposited 2008-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366 Chain B 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366	Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6；297 K；0.1 M MES, 0.1 M ammonium sulfate, 16% PEG1000, 10% glycerol, pH 6.0, hanging drop, temperature 297K	Resolution 1.75 Å R-free 0.289
3CVE Crystal Structure of the carboxy terminus of Homer1 Deposited 2008-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366 Chain D 302–366（65 aa） Fragment：Coiled-coil region, UNP residues 302-366	Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L308M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6；297 K；0.1 M MES, 0.1 M ammonium sulfate, 16% PEG1000, 10% glycerol, pH 6.0, hanging drop, temperature 297K	Resolution 1.75 Å R-free 0.289

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HOME1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 4–114

METABOTROPIC GLUTAMATE RECEPTOR MGLUR5

OrganismNot specified

UniProt P31424

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1123–1128	Fragment：MGLUR DERIVED PEPTIDE TPPSPF	GLGF-DOMAIN PROTEIN HOMER × 1 （Q9Z214）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1123–1128	Fragment：MGLUR DERIVED PEPTIDE TPPSPF	GLGF-DOMAIN PROTEIN HOMER × 2 （Q9Z214）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MGR5_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–6； UniProt 1123–1128

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	1ddv
Deposition date deposition_date	1999-11-11
Structure title title	CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE
Keywords keywords	PROTEIN-LIGAND COMPLEX, POLYPROLINE RECOGNITION, BETA TURN, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.87 Å
Radius of gyration Rg (electron density) rg_electron	13.36 Å
Forward intensity I(0) i0	3142090.00
Molecular weight molecular_weight	12533.0 kDa
Excluded volume excluded_volume	15764 Å³
Envelope volume envelope_volume	17743 Å³
Hydration-shell volume shell_volume	11359 Å³
Envelope diameter envelope_diameter	45.4 Å
Shell Rg shell_rg	19.01 Å
Envelope Rg envelope_rg	13.73 Å
Shape Rg shape_rg	13.31 Å
Total Rg total_rg	14.77 Å
Total atoms total_atoms	889
Residues n_residues	110
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	46.8 Å
Rg (real space) rg_real	14.77 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	3.1420e+06
I(0) uncertainty (real space) i0_real_error	3.6730e+04
Rg (reciprocal space) rg_reciprocal	14.78 Å
I(0) (reciprocal space) i0_reciprocal	3142000.0000
Solution quality estimate total_estimate	0.8913
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.114
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	588100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	GLGF-DOMAIN PROTEIN HOMER
Molecular weight formula_weight	12688.2 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	965

MGEQPIFSTRAHVFQIDPNTKKNWVPTSKHAVTVSYFYDSTRNVYRIISLDGSKAIINSTITPNMTFTKTSQKFGQWADSRANTVYGLGFSSEHHLSKFAEKFQEFKEAAR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	METABOTROPIC GLUTAMATE RECEPTOR MGLUR5
Molecular weight formula_weight	644.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TPPSPF

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ddva_
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)

CATH v4.4 (1 domains)

Domain ID domain_id	1ddvA00
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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8. Citations (2)

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Unit-cell length a length_a	55.700 Å
Unit-cell length b length_b	48.600 Å
Unit-cell length c length_c	35.900 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2780

fit	/app/data/saxs_computation/dd/1ddv/1ddv.fit
pddf	/app/data/pr_computation/dd/1ddv/1ddv.pr.out
profile	/app/data/saxs_computation/dd/1ddv/1ddv.dat

CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE

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

GLGF-DOMAIN PROTEIN HOMER

State in the Current Structure

Other States of the Same Protein in the Database

METABOTROPIC GLUTAMATE RECEPTOR MGLUR5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)