SAXSdb — 5eel

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

Growth factor receptor-bound protein 7

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 MALONIC ACID × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 MALONIC ACID × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 MALONIC ACID × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 MALONIC ACID × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Bicyclic Peptide Inhibitor × 1 MALONIC ACID × 1 FORMIC ACID × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GRB7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–120； UniProt 415–532 Author chain B； PDBConstruct 3–120； UniProt 415–532 Author chain C； PDBConstruct 3–120； UniProt 415–532 Author chain D； PDBConstruct 3–120； UniProt 415–532 Author chain E； PDBConstruct 3–120； UniProt 415–532 Author chain F； PDBConstruct 3–120； UniProt 415–532

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	5eel
Deposition date deposition_date	2015-10-23
Structure title title	Grb7 SH2 with bicyclic peptide inhibitor
Keywords keywords	SH2, inhibitor, bicyclic, 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.

5eel__assembly_1__model_1

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

Download this curve (.dat)

5eel__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5eel__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.56 Å
Rg (electron density)	13.13 Å
Total Rg	14.37 Å
Atom count	905
Residues	111
Excluded volume	15982 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5eel__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5eel__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5eel__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5eel__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5eel__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5eel__assembly_6__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 (6)

Entity 1 Entity 1 polymer

Description description	Growth factor receptor-bound protein 7
Molecular weight formula_weight	13690.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5572

GSPASGTSLSAAIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCTRVAL

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 polymer

Description description	Bicyclic Peptide Inhibitor
Molecular weight formula_weight	1134.2 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M,N,P,Q,R

SFEGYDNXC

Entity 3 Entity 3 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5eelA00
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	5eelB00
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	5eelC00
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	5eelD00
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	5eelE00
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	5eelF00
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	95.228 Å
Unit-cell length b length_b	95.228 Å
Unit-cell length c length_c	241.566 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	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.470 Å
Low-resolution limit resolution_low	46.720 Å
R factor r_factor	0.1880
R_work r_work	0.1850
R_free r_free	0.2320

Grb7 SH2 with bicyclic peptide inhibitor

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

Growth factor receptor-bound protein 7

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

5eel__assembly_1__model_1

5eel__assembly_1__model_1 | I(q)

5eel__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Grb7 SH2 with bicyclic peptide inhibitor

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

Growth factor receptor-bound protein 7

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

5eel__assembly_1__model_1

5eel__assembly_1__model_1 | I(q)

5eel__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)