SAXSdb — 6kc4

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

Tyrosine-protein kinase Fer

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	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	phosphopeptide (EDpYENVD) × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FER_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–102； UniProt 453–552 Author chain C； PDBConstruct 3–102； UniProt 453–552 Author chain E； PDBConstruct 3–102； UniProt 453–552 Author chain G； PDBConstruct 3–102； UniProt 453–552 Author chain I； PDBConstruct 3–102； UniProt 453–552 Author chain K； PDBConstruct 3–102； UniProt 453–552

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	6kc4
Deposition date deposition_date	2019-06-27
Structure title title	Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)
Keywords keywords	SH2 domain, SIGNALING PROTEIN, TRANSFERASE-SIGNALING PROTEIN complex; TRANSFERASE/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.

6kc4__assembly_1__model_1

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

Download this curve (.dat)

6kc4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6kc4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.25 Å
Rg (electron density)	12.71 Å
Total Rg	14.18 Å
Atom count	880
Residues	106
Excluded volume	15556 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6kc4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6kc4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6kc4__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6kc4__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6kc4__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6kc4__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 (3)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein kinase Fer
Molecular weight formula_weight	11743.3 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	6401

GSKPLAEQDWYHGAIPRIEAQELLKKQGDFLVRESHGKPGEYVLSVYSDGQRRHFIIQYVDNMYRFEGTGFSNIPQLIDHHYTTKQVITKKSGVVLLNPIPK

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	phosphopeptide (EDpYENVD)
Molecular weight formula_weight	962.8 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

DEYENVD

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1075

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6kc4A00
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	6kc4C00
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	6kc4E00
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	6kc4G00
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	6kc4I00
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	6kc4K00
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	34.700 Å
Unit-cell length b length_b	186.661 Å
Unit-cell length c length_c	50.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.370 Å
Low-resolution limit resolution_low	25.867 Å
R factor r_factor	0.1657
R_work r_work	0.1646
R_free r_free	0.1855

Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)

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

Tyrosine-protein kinase Fer

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

6kc4__assembly_1__model_1

6kc4__assembly_1__model_1 | I(q)

6kc4__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)

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

Tyrosine-protein kinase Fer

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

6kc4__assembly_1__model_1

6kc4__assembly_1__model_1 | I(q)

6kc4__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)