SAXSdb — 5qu2

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

Cytoplasmic protein NCK1

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	ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2 × 1 SULFATE ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–60； UniProt 1–59 Author chain B； PDBConstruct 2–60； UniProt 1–59

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	5qu2
Deposition date deposition_date	2019-12-13
Structure title title	Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
Keywords keywords	SH3 DOMAIN, ADAPTOR, PEPTIDE BINDING, SIGNALING PROTEIN, DOMAIN SWAP; 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.

5qu2__assembly_1__model_1

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

Download this curve (.dat)

5qu2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5qu2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.86 Å
Rg (electron density)	11.16 Å
Total Rg	12.81 Å
Atom count	568
Residues	65
Excluded volume	9993 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5qu2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5qu2__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Cytoplasmic protein NCK1
Molecular weight formula_weight	7202.1 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	1364

SMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERK

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	ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2
Molecular weight formula_weight	1019.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XPPPVPNPDYX

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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Unit-cell length a length_a	50.650 Å
Unit-cell length b length_b	63.340 Å
Unit-cell length c length_c	99.680 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	16

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	1.040 Å
Low-resolution limit resolution_low	49.890 Å
R factor r_factor	0.1679
R_work r_work	0.1659
R_free r_free	0.2051

Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY

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

Cytoplasmic protein NCK1

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

5qu2__assembly_1__model_1

5qu2__assembly_1__model_1 | I(q)

5qu2__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 (4)

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 water

7. Citations (1)

Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY

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

Cytoplasmic protein NCK1

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

5qu2__assembly_1__model_1

5qu2__assembly_1__model_1 | I(q)

5qu2__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 (4)

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 water

7. Citations (1)