SAXSdb — 1imd

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1. Protein Identity and Related Structures Protein Identity & Related Structures

INOSITOL MONOPHOSPHATASE

Homo sapiens

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 1–277 Chain B； UniProt 1–277	Not recorded	MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.60 Å

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 1IMD	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 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 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	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
1IME STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS Deposited 1994-02-08	Different ligand/ion 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 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 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
6ZK0 1.47A human IMPase with ebselen Deposited 2020-06-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–277（277 aa） Chain BBB 1–277（277 aa）	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
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 A； PDBConstruct 1–277； UniProt 1–277 Author chain B； PDBConstruct 1–277； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1imd
Deposition date deposition_date	1994-02-08
Structure title title	STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS
Keywords keywords	HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.17 Å
Radius of gyration Rg (electron density) rg_electron	23.35 Å
Forward intensity I(0) i0	58144500.00
Molecular weight molecular_weight	58957.0 kDa
Excluded volume excluded_volume	73648 Å³
Envelope volume envelope_volume	85584 Å³
Hydration-shell volume shell_volume	29921 Å³
Envelope diameter envelope_diameter	80.7 Å
Shell Rg shell_rg	31.24 Å
Envelope Rg envelope_rg	23.50 Å
Shape Rg shape_rg	23.37 Å
Total Rg total_rg	24.16 Å
Total atoms total_atoms	4107
Residues n_residues	540
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	81.0 Å
Rg (real space) rg_real	24.09 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	5.8140e+07
I(0) uncertainty (real space) i0_real_error	8.4160e+05
Rg (reciprocal space) rg_reciprocal	24.11 Å
I(0) (reciprocal space) i0_reciprocal	58150000.0000
Solution quality estimate total_estimate	0.7972
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-0.227
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25780000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	INOSITOL MONOPHOSPHATASE
Molecular weight formula_weight	30219.8 kDa
EC 编号 ec_number	3.1.3.25
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4157

MADPWQECMDYAVTLARQAGEVVCEAIKNEMNVMLKSSPVDLVTATDQKVEKMLISSIKEKYPSHSFIGEESVAAGEKSILTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFAVNKKIEFGVVYSCVEGKMYTARKGKGAFCNGQKLQVSQQEDITKSLLVTELGSSRTPETVRMVLSNMEKLFCIPVHGIRSVGTAAVNMCLVATGGADAYYEMGIHCWDVAGAGIIVTEAGGVLMDVTGGPFDLMSRRVIAANNRILAERIAKEIQVIPLQRDDED

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1imda_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d1imdb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1imdA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1imdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1imdB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1imdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

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8. Citations (3)

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Unit-cell length a length_a	85.850 Å
Unit-cell length b length_b	85.850 Å
Unit-cell length c length_c	153.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	—

fit	/app/data/saxs_computation/im/1imd/1imd.fit
pddf	/app/data/pr_computation/im/1imd/1imd.pr.out
profile	/app/data/saxs_computation/im/1imd/1imd.dat

STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS