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4fpa

Crystal Structure of recombinant human Hexokinase type I mutant D413N Glucose 6-Phosphate

Method: X-RAY DIFFRACTION Dmax: 139.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hexokinase-1

Homo sapiens

UniProt P19367

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–917 Chain B； UniProt 1–917 Mutation：D413N BGC beta-D-glucopyranose × 4 BG6 6-O-phosphono-beta-D-glucopyranose × 4 NA SODIUM ION × 4 CIT CITRIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K Resolution 2.48 Å R-free 0.256
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–917 Mutation：D413N BGC beta-D-glucopyranose × 2 BG6 6-O-phosphono-beta-D-glucopyranose × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K Resolution 2.48 Å R-free 0.256
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–917 Mutation：D413N BGC beta-D-glucopyranose × 2 BG6 6-O-phosphono-beta-D-glucopyranose × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K Resolution 2.48 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4FPA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CZA MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE, GLUCOSE-6-PHOSPHATE, AND ADP Deposited 1999-09-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain N 1–917（917 aa）
Mutation：E280A, R283A, G284Y GLC alpha-D-glucopyranose × 2 G6P 6-O-phosphono-alpha-D-glucopyranose × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；PEG 8000, SODIUM ACETATE, MES, ADP, ALUMINUM NITRATE, SODIUM FLUORIDE, MAGNESIUM ACETATE, GLUCOSE, pH 6.5, EVAPORATION, temperature 298.0K
Resolution 1.90 Å R-free 0.258
1DGK MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOSE AND ADP IN THE ACTIVE SITE Deposited 1999-11-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain N 1–917（917 aa）
Mutation：E280A, R283A, G284Y, T536A GLC alpha-D-glucopyranose × 2 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, SODIUM ACETATE, MES, ADP, GLUCOSE, GLUCOSE-6-PHOSPHATE. GROWN CRYSTALS WERE SOAKED WITH THE SAME BUFFER, BUT W/O GLUCOSE-6-PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.308
1HKB CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND GLUCOSE-6-PHOSPHATE Deposited 1997-12-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 2 G6P 6-O-phosphono-alpha-D-glucopyranose × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION; THEN SOAKED WITH 10 MM G6P AND 5 MM GLUCOSE.
Resolution 2.80 Å R-free 0.270
1HKB CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND GLUCOSE-6-PHOSPHATE Deposited 1997-12-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 2 G6P 6-O-phosphono-alpha-D-glucopyranose × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION; THEN SOAKED WITH 10 MM G6P AND 5 MM GLUCOSE.
Resolution 2.80 Å R-free 0.270
1HKC RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND PHOSPHATE Deposited 1998-07-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 2 PO4 PHOSPHATE ION × 4 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；HEXOKINASE WAS CRYSTALLIZED BY HANGING DROP METHOD AT ROOM TEMPERATURE BY MIXING 20 MG/ ML OF PROTEIN IN 25 MM POTASSIUM PHOSPHATE WITH A PRECIPITANT SOLUTION CONTAINING 5% PEG 8000 AND 0.1 M NA CACODYLATE, PH 6.5. PROTEIN SAMPLES CONTAINED A TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION.
Resolution 2.80 Å R-free 0.241
1QHA HUMAN HEXOKINASE TYPE I COMPLEXED WITH ATP ANALOGUE AMP-PNP Deposited 1999-05-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–917（917 aa）
Chain B 1–917（917 aa）
Not recorded GLC alpha-D-glucopyranose × 4 G6P 6-O-phosphono-alpha-D-glucopyranose × 4 MG MAGNESIUM ION × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.25 Å R-free 0.279
4F9O Crystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate Deposited 2012-05-19 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–914（914 aa）
Not recorded BGC beta-D-glucopyranose × 2 0NZ 2-deoxy-6-O-phosphono-beta-D-glucopyranose × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.65 Å R-free 0.258
4F9O Crystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate Deposited 2012-05-19 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–914（914 aa）
Not recorded BGC beta-D-glucopyranose × 2 0NZ 2-deoxy-6-O-phosphono-beta-D-glucopyranose × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.65 Å R-free 0.258
4FOE Crystal Structure of recombinant human Hexokinase type I with Mannose 6-Phosphate Deposited 2012-06-20 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–917（917 aa）
Chain B 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 4 M6D 6-O-phosphono-beta-D-mannopyranose × 4 NA SODIUM ION × 4 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.70 Å R-free 0.254
4FOI Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate Deposited 2012-06-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–917（917 aa）
Chain B 1–917（917 aa）
Mutation：D413N Mutation：D413N BGC beta-D-glucopyranose × 4 G16 1,6-di-O-phosphono-alpha-D-glucopyranose × 4 NA SODIUM ION × 4 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.40 Å R-free 0.273
4FOI Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate Deposited 2012-06-20 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–917（917 aa）
Mutation：D413N BGC beta-D-glucopyranose × 2 G16 1,6-di-O-phosphono-alpha-D-glucopyranose × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.40 Å R-free 0.273
4FOI Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate Deposited 2012-06-20 Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–917（917 aa）
Mutation：D413N BGC beta-D-glucopyranose × 2 G16 1,6-di-O-phosphono-alpha-D-glucopyranose × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 2.40 Å R-free 0.273
4FPB Crystal Structure of Recombinant Human Hexokinase Type I with 1,5-Anhydroglucitol 6-Phosphate Deposited 2012-06-21 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–917（917 aa）
Chain B 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 4 0WK 1,5-anhydro-6-O-phosphono-D-glucitol × 4 NA SODIUM ION × 4 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.256
4FPB Crystal Structure of Recombinant Human Hexokinase Type I with 1,5-Anhydroglucitol 6-Phosphate Deposited 2012-06-21 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 2 0WK 1,5-anhydro-6-O-phosphono-D-glucitol × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.256
4FPB Crystal Structure of Recombinant Human Hexokinase Type I with 1,5-Anhydroglucitol 6-Phosphate Deposited 2012-06-21 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–917（917 aa）
Not recorded BGC beta-D-glucopyranose × 2 0WK 1,5-anhydro-6-O-phosphono-D-glucitol × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6；277 K；PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.256

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HXK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–917； UniProt 1–917 Author chain B； PDBConstruct 1–917； UniProt 1–917

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4fpa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fpa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fpa
Deposition date deposition_date2012-06-21
Structure title titleCrystal Structure of recombinant human Hexokinase type I mutant D413N Glucose 6-Phosphate
Keywords keywordshexokinase, Glucose-6-Phosphate, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.13 Å
Radius of gyration Rg (electron density) rg_electron41.58 Å
Forward intensity I(0) i0631183000.00
Molecular weight molecular_weight203160.0 kDa
Excluded volume excluded_volume253200 ų
Envelope volume envelope_volume335310 ų
Hydration-shell volume shell_volume66133 ų
Envelope diameter envelope_diameter139.6 Å
Shell Rg shell_rg48.19 Å
Envelope Rg envelope_rg40.64 Å
Shape Rg shape_rg41.59 Å
Total Rg total_rg41.87 Å
Total atoms total_atoms14206
Residues n_residues1798
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax139.9 Å
Rg (real space) rg_real42.05 Å
Rg uncertainty (real space) rg_real_error1.40 Å
I(0) (real space) i0_real6.3120e+08
I(0) uncertainty (real space) i0_real_error1.0780e+07
Rg (reciprocal space) rg_reciprocal42.13 Å
I(0) (reciprocal space) i0_reciprocal631200000.0000
Solution quality estimate total_estimate0.8906
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.0 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60520000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.891
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4fpaa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpaa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpaa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpaa4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpab1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpab2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpab3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase
Domain ID domain_idd4fpab4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.3 — Hexokinase

CATH v4.4 (8 domains)

Domain ID domain_id4fpaA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4fpaA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id4fpaA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4fpaA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id4fpaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4fpaB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id4fpaB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4fpaB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
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8. Citations (1)

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9. Files and Curves (10)