SAXSdb — 6z2f

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

UDP-N-acetylhexosamine pyrophosphorylase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UAP1_HUMAN
Isoform	Q16222-2
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 5–509； UniProt 1–505 Author chain B； PDBConstruct 5–509； UniProt 1–505

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	6z2f
Deposition date deposition_date	2020-05-15
Structure title title	Crystal structure of human AGX1 mutant complexed with UDPGLCNAC
Keywords keywords	Hexosamine biosynthetic pathway AGX1 Disease mutant, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

6z2f__assembly_1__model_1

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

Download this curve (.dat)

6z2f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z2f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.15 Å
Rg (electron density)	35.42 Å
Total Rg	35.88 Å
Atom count	7613
Residues	943
Excluded volume	135980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z2f__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	UDP-N-acetylhexosamine pyrophosphorylase
Molecular weight formula_weight	57547.5 kDa
EC 编号 ec_number	2.7.7.83,2.7.7.23
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	8314

GPELMNINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQSSYQKNVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRTLAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRLKDANDVPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHELVKNGI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UDP-N-acetylhexosamine pyrophosphorylase
Molecular weight formula_weight	57604.5 kDa
EC 编号 ec_number	2.7.7.83,2.7.7.23
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPELMNINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQSSYQKNVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSRKTLFQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYRTLAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRLKDANDVPIQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHELVKNGI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Molecular weight formula_weight	607.4 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	701

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6z2fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.5 — UDP-glucose pyrophosphorylase

Domain ID domain_id	d6z2fb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.5 — UDP-glucose pyrophosphorylase

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Unit-cell length a length_a	45.614 Å
Unit-cell length b length_b	64.569 Å
Unit-cell length c length_c	82.070 Å
Unit-cell angle α angle_alpha	95.63 °
Unit-cell angle β angle_beta	101.09 °
Unit-cell angle γ angle_gamma	104.93 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	29.260 Å
R factor r_factor	0.1890
R_work r_work	0.1871
R_free r_free	0.2260

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC

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

UDP-N-acetylhexosamine pyrophosphorylase

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

6z2f__assembly_1__model_1

6z2f__assembly_1__model_1 | I(q)

6z2f__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC

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

UDP-N-acetylhexosamine pyrophosphorylase

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

6z2f__assembly_1__model_1

6z2f__assembly_1__model_1 | I(q)

6z2f__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)