SAXSdb — 3pe4

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

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Casein kinase II subunit alpha × 1 （P68400） URIDINE-5'-DIPHOSPHATE × 1 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Casein kinase II subunit alpha × 1 （P68400） URIDINE-5'-DIPHOSPHATE × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Casein kinase II subunit alpha × 2 （P68400） URIDINE-5'-DIPHOSPHATE × 2 SULFATE ION × 4 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Casein kinase II subunit alpha × 2 （P68400） URIDINE-5'-DIPHOSPHATE × 2 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OGT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–723； UniProt 323–1041 Author chain C； PDBConstruct 5–723； UniProt 323–1041

Casein kinase II subunit alpha

OrganismNot specified

UniProt P68400

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit × 1 （O15294） URIDINE-5'-DIPHOSPHATE × 1 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit × 1 （O15294） URIDINE-5'-DIPHOSPHATE × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit × 2 （O15294） URIDINE-5'-DIPHOSPHATE × 2 SULFATE ION × 4 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit × 2 （O15294） URIDINE-5'-DIPHOSPHATE × 2 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSK21_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–14； UniProt 340–352 Author chain D； PDBConstruct 2–14； UniProt 340–352

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	3pe4
Deposition date deposition_date	2010-10-25
Structure title title	Structure of human O-GlcNAc transferase and its complex with a peptide substrate
Keywords keywords	GT-B, glycosyltransferase, 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.

3pe4__assembly_3__model_1

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

Download this curve (.dat)

3pe4__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pe4__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	34.97 Å
Rg (electron density)	34.60 Å
Total Rg	35.17 Å
Atom count	11250
Residues	1418
Excluded volume	200180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pe4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pe4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3pe4__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3pe4__assembly_4__model_1`	tetrameric （4）	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	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Molecular weight formula_weight	80974.5 kDa
EC 编号 ec_number	2.4.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12036

GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE

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	Casein kinase II subunit alpha
Molecular weight formula_weight	1398.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

YPGGSTPVSSANMM

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	854

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3pe4A01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3pe4A02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3pe4A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11380 —

Domain ID domain_id	3pe4A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	3pe4A05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3pe4C01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3pe4C02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3pe4C03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11380 —

Domain ID domain_id	3pe4C04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	3pe4C05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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Unit-cell length a length_a	98.600 Å
Unit-cell length b length_b	136.700 Å
Unit-cell length c length_c	153.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2254
R_work r_work	0.2240
R_free r_free	0.2518

Structure of human O-GlcNAc transferase and its complex with a peptide substrate

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

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Casein kinase II subunit alpha

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

3pe4__assembly_3__model_1

3pe4__assembly_3__model_1 | I(q)

3pe4__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Structure of human O-GlcNAc transferase and its complex with a peptide substrate

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

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Casein kinase II subunit alpha

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

3pe4__assembly_3__model_1

3pe4__assembly_3__model_1 | I(q)

3pe4__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)