SAXSdb — 3agy

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

DnaJ homolog subfamily B member 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	peptide of Heat shock cognate 71 kDa protein × 3 （P11142） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNJB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–181； UniProt 161–340 Author chain B； PDBConstruct 2–181； UniProt 161–340

peptide of Heat shock cognate 71 kDa protein

OrganismNot specified

UniProt P11142

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DnaJ homolog subfamily B member 1 × 2 （P25685） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HSP7C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–8； UniProt 639–646 Author chain D； PDBConstruct 1–8； UniProt 639–646 Author chain F； PDBConstruct 1–8； UniProt 639–646

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	3agy
Deposition date deposition_date	2010-04-12
Structure title title	Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70
Keywords keywords	chaperone; CHAPERONE
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.

3agy__assembly_1__model_1

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

Download this curve (.dat)

3agy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3agy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.88 Å
Rg (electron density)	30.89 Å
Total Rg	31.56 Å
Atom count	2958
Residues	373
Excluded volume	53331 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3agy__assembly_1__model_1`	pentameric （5）	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	DnaJ homolog subfamily B member 1
Molecular weight formula_weight	20481.9 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	3220

MDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKKGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI

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	peptide of Heat shock cognate 71 kDa protein
Molecular weight formula_weight	858.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,F

GPTIEEVD

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3agyA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	3agyA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	3agyB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	3agyB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

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Unit-cell length a length_a	104.746 Å
Unit-cell length b length_b	41.132 Å
Unit-cell length c length_c	62.865 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	42.710 Å
R factor r_factor	0.2260
R_work r_work	0.2250
R_free r_free	0.2470

Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70

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

DnaJ homolog subfamily B member 1

State in the Current Structure

Other States of the Same Protein in the Database

peptide of Heat shock cognate 71 kDa protein

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

3agy__assembly_1__model_1

3agy__assembly_1__model_1 | I(q)

3agy__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70

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

DnaJ homolog subfamily B member 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

peptide of Heat shock cognate 71 kDa protein

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

3agy__assembly_1__model_1

3agy__assembly_1__model_1 | I(q)

3agy__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)