4f9o

Crystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate

Method: X-RAY DIFFRACTION Dmax: 139.0 Å Quality: GOOD

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–914 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–914 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

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.

9 other PDB entries and 16 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 1–914; UniProt 1–914 Author chain B; PDBConstruct 1–914; UniProt 1–914

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 4f9o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f9o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f9o
Deposition date deposition_date2012-05-19
Structure title titleCrystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate
Keywords keywordshexokinase, 2-deoxy Glucose-6-Phosphate, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.08
Radius of gyration Rg (electron density) rg_electron41.68
Forward intensity I(0) i01233680000.00
Molecular weight molecular_weight188530.0 kDa
Excluded volume excluded_volume180110 ų
Envelope volume envelope_volume334400 ų
Hydration-shell volume shell_volume65985 ų
Envelope diameter envelope_diameter138.8
Shell Rg shell_rg48.16
Envelope Rg envelope_rg40.65
Shape Rg shape_rg41.67
Total Rg total_rg41.91
Total atoms total_atoms14191
Residues n_residues1798
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax139.0
Rg (real space) rg_real42.01
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real1.2340e+09
I(0) uncertainty (real space) i0_real_error2.2000e+07
Rg (reciprocal space) rg_reciprocal42.08
I(0) (reciprocal space) i0_reciprocal1234000000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.2
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha59330000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.868

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4f9oa1
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_idd4f9oa2
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_idd4f9oa3
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_idd4f9oa4
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_idd4f9ob1
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_idd4f9ob2
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_idd4f9ob3
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_idd4f9ob4
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_id4f9oA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id4f9oA02
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_id4f9oA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id4f9oA04
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_id4f9oB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id4f9oB02
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_id4f9oB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id4f9oB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain

8. Citations (1)

9. Files and Curves (10)