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6zk0

1.47A human IMPase with ebselen

Method: X-RAY DIFFRACTION Dmax: 77.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inositol monophosphatase 1

Homo sapiens

UniProt P29218

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 AAA； UniProt 1–277 Chain BBB； UniProt 1–277 Not recorded NA SODIUM ION × 8 MN MANGANESE (II) ION × 6 SO4 SULFATE ION × 2 GOL GLYCEROL × 9 9JT N-phenyl-2-selanylbenzamide × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M MnS04, 0.1M MES, 28% PEG4000 and pH 5.5 Resolution 1.47 Å R-free 0.208

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 6ZK0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AWB HUMAN MYO-INOSITOL MONOPHOSPHATASE IN COMPLEX WITH D-INOSITOL-1-PHOSPHATE AND CALCIUM Deposited 1997-10-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–277（276 aa）
Chain B 2–277（276 aa）
Not recorded CA CALCIUM ION × 6 CL CHLORIDE ION × 2 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8,000, 100MM SODIUM CACODYLATE PH 6.5, 200MM CALCIUM ACETATE, 1MM EDTA, 4MM DTT, 40MM D-INOSITOL-1-PHOSPHATE, 0.1M SODIUM CACODYLATE PH 6.5
Resolution 2.50 Å R-free 0.189
1IMA STRUCTURAL ANALYSIS OF INOSITOL MONOPHOSPHATASE COMPLEXES WITH SUBSTRATES Deposited 1994-02-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded GD GADOLINIUM ATOM × 2 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1IMB STRUCTURAL ANALYSIS OF INOSITOL MONOPHOSPHATASE COMPLEXES WITH SUBSTRATES Deposited 1994-02-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded GD GADOLINIUM ATOM × 2 LIP L-MYO-INOSITOL-1-PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1IMC STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS Deposited 1994-02-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1IMD STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS Deposited 1994-02-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1IME STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS Deposited 1994-02-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å
1IMF STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS Deposited 1994-02-08 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 1–277（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
2HHM STRUCTURE OF INOSITOL MONOPHOSPHATASE, THE PUTATIVE TARGET OF LITHIUM THERAPY Deposited 1992-10-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–277（276 aa）
Chain B 2–277（276 aa）
Not recorded SO4 SULFATE ION × 2 GD GADOLINIUM ATOM × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
4AS4 Structure of human inositol monophosphatase 1 Deposited 2012-04-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 6 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；40% W/V PEG 3350 AND 0.2 M MAGNESIUM FORMATE, pH 7
Resolution 1.70 Å R-free 0.186
6GIU Human IMPase with L-690330 Deposited 2018-05-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded MN MANGANESE (II) ION × 7 L69 [1-(4-oxidanylphenoxy)-1-phosphono-ethyl]phosphonic acid × 2 GOL GLYCEROL × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Equal volumes (1uL) of the enzyme-inhibitor mix and reservoir solution (0.2 M MnSO4, 0.1 M MES pH 5.5, 25 % (w/v) PEG 4000) containing seeds (diluted 1:100 in reservoir solution) were mixed.
Resolution 1.39 Å R-free 0.167
6GJ0 Human IMPase with Mn Deposited 2018-05-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–277（277 aa）
Chain B 1–277（277 aa）
Not recorded MN MANGANESE (II) ION × 6 GOL GLYCEROL × 6 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Equal volumes (1 uL) of the protein in storage buffer (20 mg/mL) and reservoir solution (0.12 M MnSO4, 0.1 M MES pH 5.5, 24 % (w/v) PEG 4000) were mixed.
Resolution 1.73 Å R-free 0.210
7VCE Structural studies of human inositol monophosphatase-1 inhibition by ebselen Deposited 2021-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–276（274 aa）
Chain B 3–276（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.2 M magnesium formate and 20% (wt/vol) PEG 3350
Resolution 2.60 Å R-free 0.244

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IMPA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain AAA； PDBConstruct 3–279； UniProt 1–277 Author chain BBB； PDBConstruct 3–279； UniProt 1–277

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 6zk0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zk0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zk0
Deposition date deposition_date2020-06-29
Structure title title1.47A human IMPase with ebselen
Keywords keywordsInhibitor, Complex, phosphatase, HYDROLASE; HYDROLASE
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_guinier24.01 Å
Radius of gyration Rg (electron density) rg_electron23.10 Å
Forward intensity I(0) i060935700.00
Molecular weight molecular_weight60801.0 kDa
Excluded volume excluded_volume75891 ų
Envelope volume envelope_volume85157 ų
Hydration-shell volume shell_volume29959 ų
Envelope diameter envelope_diameter80.1 Å
Shell Rg shell_rg31.11 Å
Envelope Rg envelope_rg23.32 Å
Shape Rg shape_rg23.15 Å
Total Rg total_rg23.81 Å
Total atoms total_atoms4225
Residues n_residues549
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 dmax77.8 Å
Rg (real space) rg_real23.94 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real6.0940e+07
I(0) uncertainty (real space) i0_real_error7.6730e+05
Rg (reciprocal space) rg_reciprocal23.96 Å
I(0) (reciprocal space) i0_reciprocal60940000.0000
Solution quality estimate total_estimate0.8873
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.2 Å
Skewness Skewness skewness0.334
Kurtosis Kurtosis kurtosis-0.212
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23130000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)