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4r5j

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

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

Escherichia coli

UniProt P0A6Y8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 CALCIUM ION × 3 PHOSPHATE ION × 1 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 CALCIUM ION × 2 PHOSPHATE ION × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1bpr 1dg4 2bpr 2kho 4b9q 4b9q 4b9q 4b9q 4f01 4f01 4jnf 5oow

13 assemblies; showing the first 12

Homodimer
4f01 4jn4 4jne 4r5g 4r5g 4r5j 4r5j 4r5k 4r5l 4r5l

10 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1dkx 1dkx 1dky 1dky 1dky 1dkz 1dkz 1q5l 3dpo 3dpo 3dpo 3dpp

103 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNAK_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–228； UniProt 389–607 Author chain B； PDBConstruct 10–228； UniProt 389–607 Author chain C； PDBConstruct 10–228； UniProt 389–607 Author chain D； PDBConstruct 10–228； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id4r5j
Deposition date deposition_date2014-08-21
Structure title titleCrystal structure of the DnaK C-terminus (Dnak-SBD-A)
Keywords keywordsHelical bundle, beta sheets, Chaperone, membrane; CHAPERONE
Experimental Method methodX-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.

4r5j__assembly_1__model_1

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

Download this curve (.dat)

4r5j__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4r5j__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）27.58 Å
Rg (electron density)27.14 Å
Total Rg27.60 Å
Atom count3307
Residues442
Excluded volume58417 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4r5j__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4r5j__assembly_2__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 (4)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd4r5ja1
Class classb — All beta proteins
Fold Fold foldb.130 — Heat shock protein 70kD (HSP70), peptide-binding domain
Superfamily Superfamily superfamilyb.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Family Family familyb.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Domain ID domain_idd4r5ja2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family familya.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Domain ID domain_idd4r5ja3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4r5jb1
Class classb — All beta proteins
Fold Fold foldb.130 — Heat shock protein 70kD (HSP70), peptide-binding domain
Superfamily Superfamily superfamilyb.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Family Family familyb.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Domain ID domain_idd4r5jb2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family familya.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Domain ID domain_idd4r5jb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4r5jc1
Class classb — All beta proteins
Fold Fold foldb.130 — Heat shock protein 70kD (HSP70), peptide-binding domain
Superfamily Superfamily superfamilyb.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Family Family familyb.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Domain ID domain_idd4r5jc2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family familya.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Domain ID domain_idd4r5jc3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4r5jd1
Class classb — All beta proteins
Fold Fold foldb.130 — Heat shock protein 70kD (HSP70), peptide-binding domain
Superfamily Superfamily superfamilyb.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Family Family familyb.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain
Domain ID domain_idd4r5jd2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family familya.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Domain ID domain_idd4r5jd3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id4r5jA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id4r5jA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id4r5jB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id4r5jB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id4r5jC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id4r5jC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id4r5jD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id4r5jD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
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7. Citations (1)