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1sz2

Crystal structure of E. coli glucokinase in complex with glucose

Method: X-RAY DIFFRACTION Dmax: 84.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucokinase

Escherichia coli

UniProt P0A6V8

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 2–321 Chain B； UniProt 2–321 Fragment：glucokinase Non-standard monomer：Yes (specific site not provided by mmCIF) BGC beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 6000, MgCl2, Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.20 Å R-free 0.265

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 1SZ2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Q18 Crystal structure of E.coli glucokinase (Glk) Deposited 2003-07-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–321（320 aa）
Chain B 2–321（320 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；20% PEG 4000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.36 Å R-free 0.267
9YRS E. Coli Glucokinase - K214Q Deposited 2025-10-17 Different construct 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 1–321（321 aa）
Chain B 1–321（321 aa）
Mutation：K214Q Mutation：K214Q PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；297 K；100 mM MES / Sodium hydroxide pH 5.5, 100 mM Ammonium citrate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol
Resolution 2.70 Å R-free 0.190

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLK_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 13–332； UniProt 2–321 Author chain B； PDBConstruct 13–332； UniProt 2–321

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 1sz2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1sz2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1sz2
Deposition date deposition_date2004-04-02
Structure title titleCrystal structure of E. coli glucokinase in complex with glucose
Keywords keywordsglucokinase, ATP-dependent, glucose binding, 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_guinier26.92 Å
Radius of gyration Rg (electron density) rg_electron25.96 Å
Forward intensity I(0) i077959500.00
Molecular weight molecular_weight69876.0 kDa
Excluded volume excluded_volume87708 ų
Envelope volume envelope_volume105310 ų
Hydration-shell volume shell_volume33493 ų
Envelope diameter envelope_diameter88.7 Å
Shell Rg shell_rg33.78 Å
Envelope Rg envelope_rg26.19 Å
Shape Rg shape_rg25.94 Å
Total Rg total_rg26.84 Å
Total atoms total_atoms4891
Residues n_residues629
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 dmax84.8 Å
Rg (real space) rg_real26.84 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real7.7960e+07
I(0) uncertainty (real space) i0_real_error9.5990e+05
Rg (reciprocal space) rg_reciprocal26.86 Å
I(0) (reciprocal space) i0_reciprocal77960000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.0 Å
Skewness Skewness skewness0.269
Kurtosis Kurtosis kurtosis-0.391
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21380000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1sz2a2
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.55.1.7 — Glucokinase
Domain ID domain_idd1sz2a3
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.55.1.7 — Glucokinase
Domain ID domain_idd1sz2b2
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.55.1.7 — Glucokinase
Domain ID domain_idd1sz2b3
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.55.1.7 — Glucokinase

CATH v4.4 (4 domains)

Domain ID domain_id1sz2A01
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_id1sz2A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1sz2B01
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_id1sz2B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)