SAXSdb — 1rao

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

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ADENOSINE MONOPHOSPHATE × 1 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HPPK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

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	1rao
Deposition date deposition_date	2003-10-31
Structure title title	CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI HPPK WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.56 ANGSTROM RESOLUTION
Keywords keywords	;PYROPHOSPHOKINASE, PYROPHOSPHORYL TRANSFER, CATALYTIC MECHANISM, FOLATE, HPPK, PTERIN, 6-HYDROXYMETHYL-7, 8-DIHYDROPTERIN, 6-HYDROXYMETHYLPTERIN, TERNARY COMPLEX, SUBSTRATE SPECIFICITY, PRODUCT RELEASE, ANTIMICROBIAL AGENT, DRUG DESIGN, TRANSFERASE ;; 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.

1rao__assembly_1__model_1

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

Download this curve (.dat)

1rao__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rao__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.67 Å
Rg (electron density)	15.50 Å
Total Rg	16.50 Å
Atom count	1312
Residues	158
Excluded volume	23211 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rao__assembly_1__model_1`	monomeric （1）	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	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Molecular weight formula_weight	17966.5 kDa
EC 编号 ec_number	2.7.6.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1595

TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Entity 3 Entity 3 non-polymer

Description description	6-HYDROXYMETHYLPTERIN-DIPHOSPHATE
Molecular weight formula_weight	353.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1raoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.30 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK
Family Family family	d.58.30.1 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK

CATH v4.4 (1 domains)

Domain ID domain_id	1raoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

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Unit-cell length a length_a	79.689 Å
Unit-cell length b length_b	52.918 Å
Unit-cell length c length_c	36.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1203
R_work r_work	0.1274
R_free r_free	0.1875

CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI HPPK WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.56 ANGSTROM RESOLUTION

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

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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

1rao__assembly_1__model_1

1rao__assembly_1__model_1 | I(q)

1rao__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (3)

CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI HPPK WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.56 ANGSTROM RESOLUTION

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

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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

1rao__assembly_1__model_1

1rao__assembly_1__model_1 | I(q)

1rao__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (3)