SAXSdb — 3ud5

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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	5'-S-[1-(2-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine × 1 1,2-ETHANEDIOL × 2 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 2–159

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	3ud5
Deposition date deposition_date	2011-10-27
Structure title title	Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1A
Keywords keywords	Alpha Beta, Kinase, ATP Binding, Pyrophosphoryl Transfer, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

3ud5__assembly_1__model_1

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

Download this curve (.dat)

3ud5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ud5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.92 Å
Rg (electron density)	15.57 Å
Total Rg	16.63 Å
Atom count	1316
Residues	158
Excluded volume	23442 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ud5__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	1480

TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	5'-S-[1-(2-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	106

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ud5a_
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	3ud5A00
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	79.920 Å
Unit-cell length b length_b	52.840 Å
Unit-cell length c length_c	36.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.57 °
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	2.000 Å
Low-resolution limit resolution_low	29.841 Å
R factor r_factor	0.1640
R_work r_work	0.1599
R_free r_free	0.2046

Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1A

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

3ud5__assembly_1__model_1

3ud5__assembly_1__model_1 | I(q)

3ud5__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 (2)

Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1A

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

3ud5__assembly_1__model_1

3ud5__assembly_1__model_1 | I(q)

3ud5__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 (2)