5etl

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.82 angstrom resolution

Method: X-RAY DIFFRACTION

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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	CALCIUM ION × 4 ADENOSINE-5'-TRIPHOSPHATE × 1 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 3 ADENOSINE-5'-TRIPHOSPHATE × 1 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile × 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 4–162； UniProt 1–159 Author chain B； PDBConstruct 4–162； UniProt 1–159 Author chain C； PDBConstruct 4–162； UniProt 1–159 Author chain D； PDBConstruct 4–162； UniProt 1–159

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	5etl
Deposition date deposition_date	2015-11-17
Structure title title	E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.82 angstrom resolution
Keywords keywords	inhibitor, complex, ampcpp, pyrophosphokinase, 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.

5etl__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5etl__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5etl__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.09 Å
Rg (electron density)	14.88 Å
Total Rg	15.97 Å
Atom count	1297
Residues	156
Excluded volume	23107 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5etl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5etl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5etl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5etl__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Molecular weight formula_weight	18312.9 kDa
EC 编号 ec_number	2.7.6.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5768

GSAMTVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile
Molecular weight formula_weight	298.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	528

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5etla1
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

Domain ID domain_id	d5etla2
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	d5etlb1
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

Domain ID domain_id	d5etlb2
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	d5etlc1
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

Domain ID domain_id	d5etlc2
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	d5etld1
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

Domain ID domain_id	d5etld2
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

CATH v4.4 (4 domains)

Domain ID domain_id	5etlA00
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

Domain ID domain_id	5etlB00
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

Domain ID domain_id	5etlC00
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

Domain ID domain_id	5etlD00
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	69.447 Å
Unit-cell length b length_b	36.179 Å
Unit-cell length c length_c	121.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	45.810 Å
R factor r_factor	0.2042
R_work r_work	0.2024
R_free r_free	0.2407

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.82 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

5etl__assembly_3__model_1

5etl__assembly_3__model_1 | I(q)

5etl__assembly_3__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.82 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

5etl__assembly_3__model_1

5etl__assembly_3__model_1 | I(q)

5etl__assembly_3__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)