SAXSdb — 6hm3

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

S-M checkpoint control protein rad4

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA replication regulator sld3 × 1 （Q09761） GLYCEROL × 2 CALCIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD4_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 1–186

DNA replication regulator sld3

OrganismNot specified

UniProt Q09761

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	S-M checkpoint control protein rad4 × 1 （P32372） GLYCEROL × 2 CALCIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SLD3_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–30； UniProt 629–656

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	6hm3
Deposition date deposition_date	2018-09-12
Structure title title	Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphopeptide
Keywords keywords	BRCT domain phosphopeptide recognition, cell cycle; CELL CYCLE
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.

6hm3__assembly_1__model_1

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

Download this curve (.dat)

6hm3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hm3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.89 Å
Rg (electron density)	19.97 Å
Total Rg	20.88 Å
Atom count	1673
Residues	206
Excluded volume	30084 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hm3__assembly_1__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	S-M checkpoint control protein rad4
Molecular weight formula_weight	21236.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1907

MGSSKPLKGFVICCTSIDLKQRTEISTKATKLGAAYRSDFTKDVTHLIAGDFDTPKYKFAAKSRPDIKIMSSEWIPVLYESWVQGEDLDDGLLVDKHLLPTLFKCRVCLTNIGQPERSRIENYVLKHGGTFCPDLTRDVTHLIAGTSSGRKYEYALKWKINVVCVEWLWQSIQRNAVLEPQYFQLD

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA replication regulator sld3
Molecular weight formula_weight	3411.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GYDSILVQATPRKSSSVITELPDTPIKMNS

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6hm3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	6hm3A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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Unit-cell length a length_a	39.400 Å
Unit-cell length b length_b	59.170 Å
Unit-cell length c length_c	120.430 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.773 Å
Low-resolution limit resolution_low	42.204 Å
R factor r_factor	0.1935
R_work r_work	0.1917
R_free r_free	0.2278

Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphopeptide

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

S-M checkpoint control protein rad4

State in the Current Structure

Other States of the Same Protein in the Database

DNA replication regulator sld3

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

6hm3__assembly_1__model_1

6hm3__assembly_1__model_1 | I(q)

6hm3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphopeptide

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

S-M checkpoint control protein rad4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA replication regulator sld3

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

6hm3__assembly_1__model_1

6hm3__assembly_1__model_1 | I(q)

6hm3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)