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4gyy

Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate

Method: X-RAY DIFFRACTION
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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

UniProt O15294

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） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 1 SULFATE ION × 2 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Casein kinase II subunit alpha × 1 （P68400） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 1 SULFATE ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Casein kinase II subunit alpha × 2 （P68400） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 SULFATE ION × 4 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Casein kinase II subunit alpha × 2 （P68400） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 SULFATE ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3pe3 3pe3 3pe3 3pe3 4gz5 4gz5 4gz5 4gz5 4gz6 4gz6 4gz6 4gz6

15 assemblies; showing the first 12

Homodimer
1w3b 7ntf 7yea

3 assemblies

Homotetramer

None

Other homooligomers
4gz5 4gz6

2 assemblies

Heteromeric or nucleic-acid complex
3pe4 3pe4 3pe4 3pe4 3tax 3tax 3tax 3tax 4ay5 4ay5 4ay5 4ay5

82 assemblies; showing the first 12

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） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen 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） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen 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） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen 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） ;(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 SULFATE ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
11uc 1na7 1pjk 2pvr 2zjw 3amy 3at2 3at3 3at4 3axw 3bqc 3c13

375 assemblies; showing the first 12

Homodimer
3h30 3u9c 5cu3 5kwh 5oqu 5orj 5ork 5ot5 5otd 5oth 5otl 5oto

21 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jwh 3pe4 3pe4 3pe4 3pe4 3tax 3tax 3tax 3tax 3u87 3u87 4dgl

53 assemblies; showing the first 12

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_id4gyy
Deposition date deposition_date2012-09-05
Structure title titleCrystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate
Keywords keywordsOGT, O-GlcNAc, GT-B, glycosyltransferase, GlcNAcylation, transferase-peptide complex; transferase/peptide
Experimental Method methodX-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.

4gyy__assembly_1__model_1

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

Download this curve (.dat)

4gyy__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4gyy__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）28.01 Å
Rg (electron density)27.53 Å
Total Rg28.18 Å
Atom count5621
Residues707
Excluded volume99929 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4gyy__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4gyy__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4gyy__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4gyy__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)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id4gyyA01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id4gyyA02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id4gyyA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11380 —
Domain ID domain_id4gyyA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily150 —
Domain ID domain_id4gyyA05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
Domain ID domain_id4gyyC01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id4gyyC02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id4gyyC03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11380 —
Domain ID domain_id4gyyC04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily150 —
Domain ID domain_id4gyyC05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
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7. Citations (1)