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2gk1

X-ray crystal structure of NGT-bound HexA

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

Beta-hexosaminidase subunit alpha

OrganismNot specified

UniProt P06865

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit beta × 1 （P07686） Beta-hexosaminidase subunit beta chain B × 1 （P07686） Beta-hexosaminidase subunit beta chain A × 1 （P07686） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2 Consistent with protein count
2 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit beta × 1 （P07686） Beta-hexosaminidase subunit beta chain B × 1 （P07686） Beta-hexosaminidase subunit beta chain A × 1 （P07686） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2 Consistent with protein count
3 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit beta × 1 （P07686） Beta-hexosaminidase subunit beta chain B × 1 （P07686） Beta-hexosaminidase subunit beta chain A × 1 （P07686） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 Consistent with protein count
4 Other combination Heteromer Protein 10 其他Polymer 6 Beta-hexosaminidase subunit beta × 2 （P07686） Beta-hexosaminidase subunit beta chain B × 2 （P07686） Beta-hexosaminidase subunit beta chain A × 2 （P07686） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 4 water × 4 Consistent with protein count
5 Other combination Heteromer Protein 10 其他Polymer 5 Beta-hexosaminidase subunit beta × 2 （P07686） Beta-hexosaminidase subunit beta chain B × 2 （P07686） Beta-hexosaminidase subunit beta chain A × 2 （P07686） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 4 Consistent with protein count
6 Other combination Heteromer Protein 5 其他Polymer 2 Beta-hexosaminidase subunit beta × 1 （P07686） Beta-hexosaminidase subunit beta chain B × 1 （P07686） Beta-hexosaminidase subunit beta chain A × 1 （P07686） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2gjx 2gjx 2gjx 2gjx 2gjx 2gjx 2gk1 2gk1 2gk1 2gk1 2gk1 2gk1

12 assemblies

View Construct and Data Evidence
UniProt name HEXA_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–52； UniProt 23–74 Author chain C； PDBConstruct 1–52； UniProt 23–74 Author chain E； PDBConstruct 1–52； UniProt 23–74 Author chain G； PDBConstruct 1–52； UniProt 23–74 Author chain I； PDBConstruct 1–440； UniProt 89–528 Author chain J； PDBConstruct 1–440； UniProt 89–528 Author chain K； PDBConstruct 1–440； UniProt 89–528 Author chain L； PDBConstruct 1–440； UniProt 89–528

Beta-hexosaminidase subunit beta

OrganismNot specified

UniProt P07686

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit alpha × 1 （P06865） Beta-hexosaminidase subunit alpha × 1 （P06865） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2 Consistent with protein count
2 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit alpha × 1 （P06865） Beta-hexosaminidase subunit alpha × 1 （P06865） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2 Consistent with protein count
3 Other combination Heteromer Protein 5 其他Polymer 3 Beta-hexosaminidase subunit alpha × 1 （P06865） Beta-hexosaminidase subunit alpha × 1 （P06865） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 Consistent with protein count
4 Other combination Heteromer Protein 10 其他Polymer 6 Beta-hexosaminidase subunit alpha × 2 （P06865） Beta-hexosaminidase subunit alpha × 2 （P06865） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 4 water × 4 Consistent with protein count
5 Other combination Heteromer Protein 10 其他Polymer 5 Beta-hexosaminidase subunit alpha × 2 （P06865） Beta-hexosaminidase subunit alpha × 2 （P06865） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 4 Consistent with protein count
6 Other combination Heteromer Protein 5 其他Polymer 2 Beta-hexosaminidase subunit alpha × 1 （P06865） Beta-hexosaminidase subunit alpha × 1 （P06865） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1nou 1nou 1np0 1np0 1np0 1o7a 1o7a 1o7a 1o7a 2gjx 2gjx 2gjx

24 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HEXB_HUMAN
Isoform —
PDB entities 3, 4, 5
Chains and sequence ranges Author chain B； PDBConstruct 1–58； UniProt 50–107 Author chain D； PDBConstruct 1–58； UniProt 50–107 Author chain F； PDBConstruct 1–58； UniProt 50–107 Author chain H； PDBConstruct 1–58； UniProt 50–107 Author chain M； PDBConstruct 1–190； UniProt 122–311 Author chain O； PDBConstruct 1–190； UniProt 122–311 Author chain Q； PDBConstruct 1–190； UniProt 122–311 Author chain S； PDBConstruct 1–190； UniProt 122–311 Author chain N； PDBConstruct 1–237； UniProt 316–552 Author chain P； PDBConstruct 1–237； UniProt 316–552 Author chain R； PDBConstruct 1–237； UniProt 316–552 Author chain T； PDBConstruct 1–237； UniProt 316–552

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_id2gk1
Deposition date deposition_date2006-03-31
Structure title titleX-ray crystal structure of NGT-bound HexA
Keywords keywordsbeta-hexoasaminidase A, glycosidase, Tay-Sachs disease, Sandhoff disease, NAG-thazoline, GM2 gangliodosis, HYDROLASE; HYDROLASE
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.

2gk1__assembly_1__model_1

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

Download this curve (.dat)

2gk1__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.

2gk1__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）32.68 Å
Rg (electron density)31.91 Å
Total Rg32.67 Å
Atom count8028
Residues972
Excluded volume143110 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2gk1__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2gk1__assembly_2__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2gk1__assembly_3__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2gk1__assembly_4__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 2gk1__assembly_5__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 2gk1__assembly_6__model_1 pentameric （5） 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 (9)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd2gk1.1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.6
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.7
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.8
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain
Domain ID domain_idd2gk1.9
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1.a
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1.b
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1.c
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1i1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1j1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1k1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd2gk1l1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.6 — beta-N-acetylhexosaminidase catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id2gk1I02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id2gk1J02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id2gk1K02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id2gk1L02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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7. Citations (1)