SAXSdb — 3drw

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

ADP-specific phosphofructokinase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE MONOPHOSPHATE × 2 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K6PF_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–472； UniProt 1–450 Author chain B； PDBConstruct 23–472； UniProt 1–450

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	3drw
Deposition date deposition_date	2008-07-11
Structure title title	Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP
Keywords keywords	;6-phosphofructokinase, Pyrococcus horikoshii, AMP, ADP, Glycolysis, Kinase, Magnesium, Metal-binding, Transferase, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG ;; TRANSFERASE
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.

3drw__assembly_1__model_1

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

Download this curve (.dat)

3drw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3drw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.94 Å
Rg (electron density)	32.32 Å
Total Rg	32.88 Å
Atom count	7427
Residues	910
Excluded volume	133380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3drw__assembly_1__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)

Entity 1 Entity 1 polymer

Description description	ADP-specific phosphofructokinase
Molecular weight formula_weight	54495.3 kDa
EC 编号 ec_number	2.7.1.146
Mutation mutation	D17A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8028

MGSSHHHHHHSSGRENLYFQGHMIPEHLSIYTAYNANIAAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRHGS

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	576

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3drwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.3 — ADP-specific Phosphofructokinase/Glucokinase

Domain ID domain_id	d3drwa2
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	d3drwb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.3 — ADP-specific Phosphofructokinase/Glucokinase

CATH v4.4 (4 domains)

Domain ID domain_id	3drwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	3drwA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3drwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	3drwB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	68.464 Å
Unit-cell length b length_b	104.190 Å
Unit-cell length c length_c	70.844 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	41.450 Å
R factor r_factor	0.1743
R_work r_work	0.1716
R_free r_free	0.2244

Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP

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

ADP-specific phosphofructokinase

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

3drw__assembly_1__model_1

3drw__assembly_1__model_1 | I(q)

3drw__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP

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

ADP-specific phosphofructokinase

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

3drw__assembly_1__model_1

3drw__assembly_1__model_1 | I(q)

3drw__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)