SAXSdb — 8hlo

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

Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1

Mus musculus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1087–1147	Fragment：SH3 domain	Proline rich motif from MICAL1 × 1 （Q8TDZ2） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；289.15 K；0.1M HEPES, pH 7.5, 1.4M Sodium citrate tribasic dihydrate	Resolution 1.17 Å R-free 0.142

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 8HLO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5C6R Crystal structure of PH domain of ASAP1 Deposited 2015-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 325–451（127 aa） Fragment：PH domain	Not recorded	PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；100 mM Na2HPO4, 100 mM Tris, pH 8.0 and 48% PEG400 (v/v)	Resolution 1.80 Å R-free 0.260
5C6R Crystal structure of PH domain of ASAP1 Deposited 2015-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 325–451（127 aa） Fragment：PH domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；100 mM Na2HPO4, 100 mM Tris, pH 8.0 and 48% PEG400 (v/v)	Resolution 1.80 Å R-free 0.260
5C79 PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2 Deposited 2015-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 325–451（127 aa） Fragment：PH domain	Not recorded	PBU (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M HEPES, pH 7.5, 15% PEG 3350	Resolution 1.60 Å R-free 0.233
5C79 PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2 Deposited 2015-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 325–451（127 aa） Fragment：PH domain	Not recorded	PBU (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M HEPES, pH 7.5, 15% PEG 3350	Resolution 1.60 Å R-free 0.233
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1083–1147（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1083–1147（65 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1083–1147（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1083–1147（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ASAP1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–67； UniProt 1087–1147

Proline rich motif from MICAL1

Homo sapiens

UniProt Q8TDZ2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 828–836	Not recorded	Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1 × 1 （Q9QWY8） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；289.15 K；0.1M HEPES, pH 7.5, 1.4M Sodium citrate tribasic dihydrate	Resolution 1.17 Å R-free 0.142

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 8HLO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WYL Solution structure of the CH domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 510–612（103 aa） Fragment：CH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.22mM CH domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CO8 Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 687–755（69 aa） Fragment：LIM domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM LIM domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2DK9 Solution structure of Calponin Homology domain of Human MICAL-1 Deposited 2006-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 506–614（109 aa） Fragment：Calponin Homology domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition 1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 100% D2O \| 100% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O \| 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O	Resolution not provided
5LE0 MICAL1 Cterminal domain Deposited 2016-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 918–1067（150 aa） Fragment：UNP residues 918-1067	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；290 K；EG	Resolution 3.30 Å R-free 0.306
5LPN Structure of human Rab10 in complex with the bMERB domain of Mical-1 Deposited 2016-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 918–1067（150 aa） Fragment：UNP residues 918-1067	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；6%-10% PEG8000 0.1M Imidazole	Resolution 2.80 Å R-free 0.287
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
8Y6K Cryo-EM structure of full-length MICAL1 in the autoinhibited state Deposited 2024-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	ZN ZINC ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris, pH 7.5, 100 mM NaCl, 2 mM MgCl2, 2 mM DTT. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9EWY CryoEM structure of human MICAL1 Deposited 2024-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9G0C Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex. Deposited 2024-07-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 918–1067（150 aa）	Mutation：V978A, V985A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.17 M Sodium acetate, 0.085 M Tris-HCl pH 8.5, 25.5% (w/v) PEG 4000 and 15% (v/v) glycerol	Resolution 1.80 Å R-free 0.231
9G0D Structure of human Mical1 bMERB_V978A domain:Rab10 complex. Deposited 2024-07-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 918–1067（150 aa）	Mutation：V978A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Imidazole pH 8.0, 5% (w/v) PEG 3000 and 30% (v/v) PEG 200	Resolution 2.05 Å R-free 0.249

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MICA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–13； UniProt 828–836

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	8hlo
Deposition date deposition_date	2022-11-30
Structure title title	Crystal structure of ASAP1-SH3 and MICAL1-PRM complex
Keywords keywords	SH3, Proline-rich motif, high-affinity, PROTEIN BINDING; PROTEIN BINDING
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	13.48 Å
Radius of gyration Rg (electron density) rg_electron	11.97 Å
Forward intensity I(0) i0	1889000.00
Molecular weight molecular_weight	9024.0 kDa
Excluded volume excluded_volume	11131 Å³
Envelope volume envelope_volume	12615 Å³
Hydration-shell volume shell_volume	9195 Å³
Envelope diameter envelope_diameter	46.1 Å
Shell Rg shell_rg	17.44 Å
Envelope Rg envelope_rg	12.51 Å
Shape Rg shape_rg	11.95 Å
Total Rg total_rg	13.35 Å
Total atoms total_atoms	1227
Residues n_residues	80
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	44.8 Å
Rg (real space) rg_real	13.41 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	1.8890e+06
I(0) uncertainty (real space) i0_real_error	2.0720e+04
Rg (reciprocal space) rg_reciprocal	13.42 Å
I(0) (reciprocal space) i0_reciprocal	1889000.0000
Solution quality estimate total_estimate	0.7956
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.207
Kurtosis Kurtosis kurtosis	-0.197
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	367500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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	Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Molecular weight formula_weight	7641.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1411

GPGSEFVRRVKTIYDCQADNDDELTFIEGEVIIVTGEEDQEWWIGHIEGQPERKGVFPVSFVHILSD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Proline rich motif from MICAL1
Molecular weight formula_weight	1304.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPGSEPPPKPPRS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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8. Citations (2)

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Unit-cell length a length_a	45.181 Å
Unit-cell length b length_b	45.181 Å
Unit-cell length c length_c	59.391 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	6

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	1.168 Å
Low-resolution limit resolution_low	39.128 Å
R factor r_factor	0.1143
R_work r_work	0.1114
R_free r_free	0.1424

fit	/app/data/saxs_computation/hl/8hlo/8hlo.fit
pddf	/app/data/pr_computation/hl/8hlo/8hlo.pr.out
profile	/app/data/saxs_computation/hl/8hlo/8hlo.dat

Crystal structure of ASAP1-SH3 and MICAL1-PRM complex

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

Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Proline rich motif from MICAL1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)