SAXSdb — 5zz9

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

Homer protein homolog 2

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptide from Drebrin × 1 （Q16643） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peptide from Drebrin × 1 （Q16643） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peptide from Drebrin × 1 （Q16643） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HOME2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–123； UniProt 1–115 Author chain B； PDBConstruct 9–123； UniProt 1–115 Author chain C； PDBConstruct 9–123； UniProt 1–115

Peptide from Drebrin

Homo sapiens

UniProt Q16643

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Homer protein homolog 2 × 1 （Q9QWW1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Homer protein homolog 2 × 1 （Q9QWW1） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Homer protein homolog 2 × 1 （Q9QWW1） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DREB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–22； UniProt 530–551 Author chain E； PDBConstruct 1–22； UniProt 530–551 Author chain F； PDBConstruct 1–22； UniProt 530–551

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	5zz9
Deposition date deposition_date	2018-05-31
Structure title title	Crystal structure of Homer2 EVH1/Drebrin PPXXF complex
Keywords keywords	POLYPROLINE RECOGNITION, SIGNALING PROTEIN, PROTEIN BINDING; PROTEIN BINDING
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.

5zz9__assembly_1__model_1

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

Download this curve (.dat)

5zz9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zz9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.86 Å
Rg (electron density)	14.43 Å
Total Rg	15.62 Å
Atom count	1020
Residues	133
Excluded volume	17957 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zz9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5zz9__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5zz9__assembly_3__model_1`	dimeric （2）	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	Homer protein homolog 2
Molecular weight formula_weight	13549.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2969

GGSGGSGGMGEQPIFTTRAHVFQIDPSTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAARLARD

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide from Drebrin
Molecular weight formula_weight	3090.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

LLNFDELPEPPATFCDPEEVEGSGENLQ

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5zz9a_
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	d5zz9b_
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	d5zz9c_
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 (3 domains)

Domain ID domain_id	5zz9A00
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)

Domain ID domain_id	5zz9B00
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)

Domain ID domain_id	5zz9C00
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	45.337 Å
Unit-cell length b length_b	47.808 Å
Unit-cell length c length_c	50.415 Å
Unit-cell angle α angle_alpha	70.44 °
Unit-cell angle β angle_beta	83.56 °
Unit-cell angle γ angle_gamma	90.39 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.153 Å
R factor r_factor	0.1934
R_work r_work	0.1916
R_free r_free	0.2281

Crystal structure of Homer2 EVH1/Drebrin PPXXF complex

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

Homer protein homolog 2

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Drebrin

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

5zz9__assembly_1__model_1

5zz9__assembly_1__model_1 | I(q)

5zz9__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Homer2 EVH1/Drebrin PPXXF complex

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

Homer protein homolog 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptide from Drebrin

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

5zz9__assembly_1__model_1

5zz9__assembly_1__model_1 | I(q)

5zz9__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)