SAXSdb — 1dkz

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

SUBSTRATE BINDING DOMAIN OF DNAK

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	SUBSTRATE PEPTIDE (7 RESIDUES) × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	SUBSTRATE PEPTIDE (7 RESIDUES) × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 388–606

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	1dkz
Deposition date deposition_date	1996-06-03
Structure title title	THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 1 NATIVE CRYSTALS
Keywords keywords	DNAK, HEAT SHOCK PROTEIN 70 KDA (HSP70), COMPLEX (MOLECULAR CHAPERONE-PEPTIDE), COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) complex; COMPLEX (MOLECULAR CHAPERONE/PEPTIDE)
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.

1dkz__assembly_1__model_1

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

Download this curve (.dat)

1dkz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dkz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.40 Å
Rg (electron density)	22.52 Å
Total Rg	23.36 Å
Atom count	3278
Residues	444
Excluded volume	58083 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dkz__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dkz__assembly_2__model_1`	octameric （8）	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	SUBSTRATE BINDING DOMAIN OF DNAK
Molecular weight formula_weight	23806.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1862

VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVSIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Entity 2 Entity 2 polymer

Description description	SUBSTRATE PEPTIDE (7 RESIDUES)
Molecular weight formula_weight	786.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NRLLLTG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dkza1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family family	a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain

Domain ID domain_id	d1dkza2
Class class	b — All beta proteins
Fold Fold fold	b.130 — Heat shock protein 70kD (HSP70), peptide-binding domain
Superfamily Superfamily superfamily	b.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Family Family family	b.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1dkzA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Substrate Binding Domain Of DNAk; Chain A, domain 1

Domain ID domain_id	1dkzA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	94.400 Å
Unit-cell length b length_b	116.700 Å
Unit-cell length c length_c	37.300 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2740

THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 1 NATIVE CRYSTALS

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

SUBSTRATE BINDING DOMAIN OF DNAK

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

1dkz__assembly_1__model_1

1dkz__assembly_1__model_1 | I(q)

1dkz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 1 NATIVE CRYSTALS

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

SUBSTRATE BINDING DOMAIN OF DNAK

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

1dkz__assembly_1__model_1

1dkz__assembly_1__model_1 | I(q)

1dkz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)