SAXSdb — 3imd

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

Growth factor receptor-bound protein 2

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	N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CHLORIDE ION × 3 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 2 CHLORIDE ION × 4 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GRB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 53–163 Author chain B； PDBConstruct 1–111； UniProt 53–163

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	3imd
Deposition date deposition_date	2009-08-10
Structure title title	Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic
Keywords keywords	;ligand preorganization, peptide mimics, Golgi apparatus, Host-virus interaction, Phosphoprotein, SH2 domain, SIGNALING PROTEIN, SIGNALING PROTEIN-pseudopeptide ligand complex, SIGNALING PROTEIN-PEPTIDE COMPLEX ;; SIGNALING PROTEIN/PEPTIDE
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.

3imd__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3imd__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3imd__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	18.59 Å
Rg (electron density)	17.36 Å
Total Rg	18.42 Å
Atom count	1745
Residues	202
Excluded volume	30876 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3imd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3imd__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3imd__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 (5)

Entity 1 Entity 1 polymer

Description description	Growth factor receptor-bound protein 2
Molecular weight formula_weight	13758.5 kDa
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	1943

IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPTYVQAHHHHHH

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	N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide
Molecular weight formula_weight	558.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3imda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d3imdb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

CATH v4.4 (2 domains)

Domain ID domain_id	3imdA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	3imdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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Unit-cell length a length_a	42.239 Å
Unit-cell length b length_b	42.243 Å
Unit-cell length c length_c	110.384 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1990
R_free r_free	0.2370

Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic

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

Growth factor receptor-bound protein 2

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

3imd__assembly_3__model_1

3imd__assembly_3__model_1 | I(q)

3imd__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic

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

Growth factor receptor-bound protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3imd__assembly_3__model_1

3imd__assembly_3__model_1 | I(q)

3imd__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)