SAXSdb — 2qx0

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

7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase

Yersinia pestis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 4 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7CKD7_YERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159 Author chain B； PDBConstruct 1–159； 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	2qx0
Deposition date deposition_date	2007-08-10
Structure title title	Crystal Structure of Yersinia pestis HPPK (Ternary Complex)
Keywords keywords	3-layered alpha-bata-alpha fold, homodimer, ternary complex, Kinase, 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.

2qx0__assembly_1__model_1

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

Download this curve (.dat)

2qx0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qx0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.05 Å
Rg (electron density)	19.44 Å
Total Rg	20.34 Å
Atom count	2624
Residues	316
Excluded volume	46668 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qx0__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 (5)

Entity 1 Entity 1 polymer

Description description	7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
Molecular weight formula_weight	18007.8 kDa
EC 编号 ec_number	2.7.6.3
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	3089

MIRVYIALGSNLAMPLQQVSAAREALAHLPRSRLVACSPLYRTKPLGPQDQPDFLNAVVALDTSLPPEQLLDHTQAIERNQGRVRKEQRWGPRTLDLDIMLYGDQVIKTDRLTIPHYGLKAREFMLYPLADIAPDLIFPDGESLSECLKRVDKNGLVLW

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	465

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qx0a_
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	d2qx0b_
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 (2 domains)

Domain ID domain_id	2qx0A00
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	2qx0B00
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	43.400 Å
Unit-cell length b length_b	78.620 Å
Unit-cell length c length_c	52.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.72 °
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	1.800 Å
Low-resolution limit resolution_low	28.900 Å
R factor r_factor	0.2320
R_work r_work	0.2300
R_free r_free	0.2690

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)

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

7,8-dihydro-6-hydroxymethylpterin-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

2qx0__assembly_1__model_1

2qx0__assembly_1__model_1 | I(q)

2qx0__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)

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

7,8-dihydro-6-hydroxymethylpterin-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

2qx0__assembly_1__model_1

2qx0__assembly_1__model_1 | I(q)

2qx0__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)