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1xxi

ADP Bound E. coli Clamp Loader Complex

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

DNA polymerase III, delta subunit

Escherichia coli

UniProt P28630

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 DNA polymerase III subunit gamma × 3 （P06710） DNA polymerase III, delta prime subunit × 1 （P28631） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 DNA polymerase III subunit gamma × 3 （P06710） DNA polymerase III, delta prime subunit × 1 （P28631） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jqj 1jqj 1jqj 1jqj 1jqj 1jql 1jr3 1xxh 1xxh 1xxi 1xxi 3glf

47 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HOLA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–343； UniProt 1–343 Author chain F； PDBConstruct 1–343； UniProt 1–343

DNA polymerase III subunit gamma

Escherichia coli

UniProt P06710

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 DNA polymerase III, delta subunit × 1 （P28630） DNA polymerase III, delta prime subunit × 1 （P28631） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 DNA polymerase III, delta subunit × 1 （P28630） DNA polymerase III, delta prime subunit × 1 （P28631） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1njf 1njf 1njf 1njf 1njg 1njg 2aya

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jr3 1xxh 1xxh 1xxi 1xxi 3glf 3glf 3glg 3glg 3glh 3glh 3glh

43 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPO3X_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–368； UniProt 1–368 Author chain C； PDBConstruct 1–368； UniProt 1–368 Author chain D； PDBConstruct 1–368； UniProt 1–368 Author chain G； PDBConstruct 1–368； UniProt 1–368 Author chain H； PDBConstruct 1–368； UniProt 1–368 Author chain I； PDBConstruct 1–368； UniProt 1–368

DNA polymerase III, delta prime subunit

Escherichia coli

UniProt P28631

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 DNA polymerase III, delta subunit × 1 （P28630） DNA polymerase III subunit gamma × 3 （P06710） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 PHOSPHATE ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 DNA polymerase III, delta subunit × 1 （P28630） DNA polymerase III subunit gamma × 3 （P06710） ZINC ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1a5t

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jr3 1xxh 1xxh 1xxi 1xxi 3glf 3glf 3glg 3glg 3glh 3glh 3glh

41 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HOLB_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–334； UniProt 1–334 Author chain J； PDBConstruct 1–334； UniProt 1–334

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_id1xxi
Deposition date deposition_date2004-11-05
Structure title titleADP Bound E. coli Clamp Loader Complex
Keywords keywordsAAA+ ATPase, clamp loader, DNA polymerase III, DNA replication, TRANSFERASE; TRANSFERASE
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.

1xxi__assembly_1__model_1

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

Download this curve (.dat)

1xxi__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1xxi__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）40.19 Å
Rg (electron density)39.21 Å
Total Rg39.67 Å
Atom count13860
Residues1766
Excluded volume247160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1xxi__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1xxi__assembly_2__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 (6)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd1xxia1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxia2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxib1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxib2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxic1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxic2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxid1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxid2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxie1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxie2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxif1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxif2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxig1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxig2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxih1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxih2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxii1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxii2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1xxij1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1xxij2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
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7. Citations (1)