1iqp

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

Method: X-RAY DIFFRACTION

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

RFCS

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-DIPHOSPHATE × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFCS_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 60–327； UniProt 1–268 Author chain B； PDBConstruct 60–327； UniProt 1–268 Author chain C； PDBConstruct 60–327； UniProt 1–268 Author chain D； PDBConstruct 60–327； UniProt 1–268 Author chain E； PDBConstruct 60–327； UniProt 1–268 Author chain F； PDBConstruct 60–327； UniProt 1–268

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	1iqp
Deposition date deposition_date	2001-07-24
Structure title title	Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Keywords keywords	CLAMP LOADER, EXTENDED AAA-ATPASE DOMAIN, COMPLEX WITH ADP, REPLICATION; REPLICATION
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.

1iqp__assembly_1__model_1

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

Download this curve (.dat)

1iqp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iqp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.29 Å
Rg (electron density)	42.62 Å
Total Rg	42.85 Å
Atom count	15787
Residues	1949
Excluded volume	283440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iqp__assembly_1__model_1`	hexameric （6）	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	RFCS
Molecular weight formula_weight	37458.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16031

MSEEIREVKVLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQLEALLAQFTLIGKK

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1iqpa1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1iqpb1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1iqpc1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1iqpd1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1iqpe1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1iqpf1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1iqpf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (18 domains)

Domain ID domain_id	1iqpA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1iqpB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1iqpC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1iqpD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1iqpE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpE03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1iqpF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1iqpF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1iqpF03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	98.361 Å
Unit-cell length b length_b	105.608 Å
Unit-cell length c length_c	316.898 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	24

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2770

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

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

RFCS

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

1iqp__assembly_1__model_1

1iqp__assembly_1__model_1 | I(q)

1iqp__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (3)

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

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

RFCS

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

1iqp__assembly_1__model_1

1iqp__assembly_1__model_1 | I(q)

1iqp__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (3)