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1q18

Crystal structure of E.coli glucokinase (Glk)

Method: X-RAY DIFFRACTION Dmax: 86.1 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 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 1Q18 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1SZ2 Crystal structure of E. coli glucokinase in complex with glucose Deposited 2004-04-02 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） Fragment：glucokinase
Chain B 2–321（320 aa） Fragment：glucokinase
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
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 1q18

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q18
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1q18
Deposition date deposition_date2003-07-18
Structure title titleCrystal structure of E.coli glucokinase (Glk)
Keywords keywords;glucokinase, ATP, kinase, phosphotransfer, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, 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_guinier27.54 Å
Radius of gyration Rg (electron density) rg_electron26.59 Å
Forward intensity I(0) i077086600.00
Molecular weight molecular_weight69634.0 kDa
Excluded volume excluded_volume87415 ų
Envelope volume envelope_volume106280 ų
Hydration-shell volume shell_volume33341 ų
Envelope diameter envelope_diameter90.1 Å
Shell Rg shell_rg34.15 Å
Envelope Rg envelope_rg26.73 Å
Shape Rg shape_rg26.57 Å
Total Rg total_rg27.44 Å
Total atoms total_atoms4875
Residues n_residues630
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 dmax86.1 Å
Rg (real space) rg_real27.46 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real7.7090e+07
I(0) uncertainty (real space) i0_real_error1.0980e+06
Rg (reciprocal space) rg_reciprocal27.49 Å
I(0) (reciprocal space) i0_reciprocal77090000.0000
Solution quality estimate total_estimate0.9047
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.421
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19740000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.939
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1q18a1
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_idd1q18a2
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_idd1q18b1
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_idd1q18b2
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_id1q18A01
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_id1q18A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1q18B01
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_id1q18B02
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)