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4d0z

GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2

HOMO SAPIENS

UniProt Q10471

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 PEPTIDE × 1 MANGANESE (II) ION × 1 1,2-ETHANEDIOL × 8 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 1 1,2-ETHANEDIOL × 10 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 1 1,2-ETHANEDIOL × 5 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 PEPTIDE × 1 MANGANESE (II) ION × 1 1,2-ETHANEDIOL × 14 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose × 1 ;(2R,3R,4R,5R,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 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2ffv 2ffv 4d0z 4d0z 4d0z 4d0z 4d11 6egs 6egs

9 assemblies

Homodimer
4d0t 5fv9 5fv9 5fv9 5fv9 5ndf 5ndf 5ndf 5ndf 5ndf 6nqt 6nqt

13 assemblies; showing the first 12

Homotetramer
2ffv

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ffu 4d0t 4d0t 4d0z 4d0z 4d11 4d11 4d11 5ajn 5ajo 5ajp 6e7i

12 assemblies

View Construct and Data Evidence
UniProt name GALT2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–571； UniProt 1–571 Author chain B； PDBConstruct 1–571； UniProt 1–571 Author chain C； PDBConstruct 1–571； UniProt 1–571 Author chain D； PDBConstruct 1–571； UniProt 1–571 Author chain E； PDBConstruct 1–571； UniProt 1–571 Author chain F； PDBConstruct 1–571； UniProt 1–571

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_id4d0z
Deposition date deposition_date2014-04-30
Structure title titleGalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)
Keywords keywords;TRANSFERASE-PEPTIDE COMPLEX, RETAINING GALNAC-T2, SUBSTRATE-GUIDED SNI-TYPE REACTION, QM/MM METADYNAMICS, BI-BI KINETIC MECHANISM, SUBSTRATE SPECIFICITY, ACETAMIDO GROUP ;; 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.

4d0z__assembly_1__model_1

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

Download this curve (.dat)

4d0z__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4d0z__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）26.57 Å
Rg (electron density)25.83 Å
Total Rg26.56 Å
Atom count4086
Residues501
Excluded volume72214 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4d0z__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4d0z__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4d0z__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4d0z__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 4d0z__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 4d0z__assembly_6__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 (7)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id4d0zA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zA02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4d0zB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zB02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4d0zC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zC02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4d0zD01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zD02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4d0zE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zE02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4d0zF01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id4d0zF02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
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7. Citations (1)