SAXSdb — 3va4

▼

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

Mediator of DNA damage checkpoint protein 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Serine/threonine-protein kinase Chk2 × 1 （O96017） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDC1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–132； UniProt 29–139 Author chain B； PDBConstruct 22–132； UniProt 29–139

Serine/threonine-protein kinase Chk2

OrganismNot specified

UniProt O96017

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Mediator of DNA damage checkpoint protein 1 × 2 （Q5PSV9） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHK2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–11； UniProt 63–73

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3va4
Deposition date deposition_date	2011-12-28
Structure title title	Crystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide
Keywords keywords	CELL CYCLE, FHA domain, DNA-damage, CHK2 and MDC1 dimerization; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3va4__assembly_1__model_1

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

Download this curve (.dat)

3va4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3va4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.29 Å
Rg (electron density)	18.40 Å
Total Rg	19.38 Å
Atom count	1782
Residues	226
Excluded volume	31786 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3va4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Mediator of DNA damage checkpoint protein 1
Molecular weight formula_weight	14589.7 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	1935

MGSSHHHHHHSSGLVPRGSHMEPIGQLRLFSGTHGPERDFPLYLGKNVVGRSPDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQELILFADFPCQYHRLDVPPPL

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein kinase Chk2
Molecular weight formula_weight	1349.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

LETVSTQELYS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3va4A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3va4B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	28.508 Å
Unit-cell length b length_b	70.224 Å
Unit-cell length c length_c	101.335 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	1.540 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1616
R_work r_work	0.1593
R_free r_free	0.2046

Crystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide

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

Mediator of DNA damage checkpoint protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase Chk2

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

3va4__assembly_1__model_1

3va4__assembly_1__model_1 | I(q)

3va4__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide

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

Mediator of DNA damage checkpoint protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase Chk2

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

3va4__assembly_1__model_1

3va4__assembly_1__model_1 | I(q)

3va4__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)