SAXSdb — 6bw6

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

UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase

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	Tunicamycin × 2 (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	Tunicamycin × 2 (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GPT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–408； UniProt 1–408 Author chain B； PDBConstruct 1–408； UniProt 1–408 Author chain C； PDBConstruct 1–408； UniProt 1–408 Author chain D； PDBConstruct 1–408； UniProt 1–408

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	6bw6
Deposition date deposition_date	2017-12-14
Structure title title	Human GPT (DPAGT1) H129 variant in complex with tunicamycin
Keywords keywords	N-linked glycosylation, endoplasmic reticulum, tunicamycin, natural product, TRANSFERASE, TRANSFERASE-ANTIBIOTIC complex; TRANSFERASE/ANTIBIOTIC
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.

6bw6__assembly_1__model_1

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

Download this curve (.dat)

6bw6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bw6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.62 Å
Rg (electron density)	27.60 Å
Total Rg	28.45 Å
Atom count	11735
Residues	742
Excluded volume	107540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bw6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6bw6__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Molecular weight formula_weight	47201.9 kDa
EC 编号 ec_number	2.7.8.15
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	23372

MWAFSELPMPLLINLIVSLLGFVATVTLIPAFRGHFIAARLCGQDLNKTSRQQIPESQGVISGAVFLIILFCFIPFPFLNCFVKEQCKAFPHHEFVALIGALLAICCMIFLGFADDVLNLRWRHKLLLHTAASLPLLMVYFTNFGNTTIVVPKPFRPILGLHLDLGILYYVYMGLLAVFCTNAINILAGINGLEAGQSLVISASIIVFNLVELEGDCRDDHVFSLYFMIPFFFTTLGLLYHNWYPSRVFVGDTFCYFAGMTFAVVGILGHFSKTMLLFFMPQVFNFLYSLPQLLHIIPCPRHRIPRLNIKTGKLEMSYSKFKTKSLSFLGTFILKVAESLQLVTVHQSETEDGEFTECNNMTLINLLLKVLGPIHERNLTLLLLLLQILGSAITFSIRYQLVRLFYDVTNSLEVLFQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	Tunicamycin
Molecular weight formula_weight	816.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	749.0 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	210.615 Å
Unit-cell length b length_b	105.363 Å
Unit-cell length c length_c	148.080 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	94.509 Å
R factor r_factor	0.2614
R_work r_work	0.2599
R_free r_free	0.2908

Human GPT (DPAGT1) H129 variant in complex with tunicamycin

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

UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase

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

6bw6__assembly_1__model_1

6bw6__assembly_1__model_1 | I(q)

6bw6__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

Human GPT (DPAGT1) H129 variant in complex with tunicamycin

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

UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase

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

6bw6__assembly_1__model_1

6bw6__assembly_1__model_1 | I(q)

6bw6__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)