4r5l

Crystal structure of the DnaK C-terminus (Dnak-SBD-C)

Method: X-RAY DIFFRACTION

▼

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

Chaperone protein DnaK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 6 PHOSPHATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 PHOSPHATE ION × 1 CALCIUM ION × 1 water × 2	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 12–230； UniProt 389–607 Author chain B； PDBConstruct 12–230； UniProt 389–607 Author chain C； PDBConstruct 12–230； UniProt 389–607 Author chain D； PDBConstruct 12–230； UniProt 389–607

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	4r5l
Deposition date deposition_date	2014-08-21
Structure title title	Crystal structure of the DnaK C-terminus (Dnak-SBD-C)
Keywords keywords	Helical bundle, beta sheets, Chaperone, membrane; CHAPERONE
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.

4r5l__assembly_1__model_1

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

Download this curve (.dat)

4r5l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r5l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.21 Å
Rg (electron density)	25.78 Å
Total Rg	26.26 Å
Atom count	3283
Residues	448
Excluded volume	57436 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r5l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4r5l__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Chaperone protein DnaK
Molecular weight formula_weight	25237.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6651

MHHHHHHIEGRVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4r5la1
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

Domain ID domain_id	d4r5la2
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	d4r5la3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4r5lb1
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

Domain ID domain_id	d4r5lb2
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	d4r5lb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4r5lc1
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

Domain ID domain_id	d4r5lc2
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	d4r5lc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4r5ld1
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

Domain ID domain_id	d4r5ld2
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	d4r5ld3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	4r5lA01
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	4r5lA02
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 —

Domain ID domain_id	4r5lB01
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	4r5lB02
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 —

Domain ID domain_id	4r5lC01
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	4r5lC02
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 —

Domain ID domain_id	4r5lD01
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	4r5lD02
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 —

▶

Unit-cell length a length_a	92.313 Å
Unit-cell length b length_b	99.906 Å
Unit-cell length c length_c	133.718 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	16

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

Resolution resolution	2.970 Å
Low-resolution limit resolution_low	41.901 Å
R factor r_factor	0.2069
R_work r_work	0.2049
R_free r_free	0.2430

Crystal structure of the DnaK C-terminus (Dnak-SBD-C)

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

Chaperone protein 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

4r5l__assembly_1__model_1

4r5l__assembly_1__model_1 | I(q)

4r5l__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the DnaK C-terminus (Dnak-SBD-C)

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

Chaperone protein 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

4r5l__assembly_1__model_1

4r5l__assembly_1__model_1 | I(q)

4r5l__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)