SAXSdb — 5c79

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

Arf-GAP

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 325–451	Fragment：PH domain	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 325–451	Fragment：PH domain	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

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 5C79	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 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 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
8HLO Crystal structure of ASAP1-SH3 and MICAL1-PRM complex Deposited 2022-11-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1087–1147（61 aa） Fragment：SH3 domain	Not recorded	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
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ASAP1_MOUSE
Isoform	Q9QWY8-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–150； UniProt 325–451 Author chain B； PDBConstruct 24–150； UniProt 325–451

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	5c79
Deposition date deposition_date	2015-06-24
Structure title title	PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2
Keywords keywords	PH domain, diC4-PtdIns(4, 5)P2, SIGNALING PROTEIN; SIGNALING PROTEIN
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	21.09 Å
Radius of gyration Rg (electron density) rg_electron	20.64 Å
Forward intensity I(0) i0	13205900.00
Molecular weight molecular_weight	25609.0 kDa
Excluded volume excluded_volume	31505 Å³
Envelope volume envelope_volume	39940 Å³
Hydration-shell volume shell_volume	17111 Å³
Envelope diameter envelope_diameter	78.9 Å
Shell Rg shell_rg	25.89 Å
Envelope Rg envelope_rg	20.95 Å
Shape Rg shape_rg	20.60 Å
Total Rg total_rg	21.52 Å
Total atoms total_atoms	1783
Residues n_residues	207
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	77.8 Å
Rg (real space) rg_real	21.21 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.3210e+07
I(0) uncertainty (real space) i0_real_error	1.6470e+05
Rg (reciprocal space) rg_reciprocal	21.19 Å
I(0) (reciprocal space) i0_reciprocal	13210000.0000
Solution quality estimate total_estimate	0.8077
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.527
Kurtosis Kurtosis kurtosis	-0.109
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2751000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.718; Smooth: 0.995

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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
Molecular weight formula_weight	17253.2 kDa
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	2005

MGHHHHHHHHHHSSGHIDDDKHMGGYSMHQLQGNKEYGSEKKGFLLKKSDGIRKVWQRRKCAVKNGILTISHATSNRQPAKLNLLTCQVKPNAEDKKSFDLISHNRTYHFQAEDEQDYIAWISVLTNSKEEALTMAFRGEQSTGENSLED

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	634.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	222

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5c79A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	5c79B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	37.543 Å
Unit-cell length b length_b	64.697 Å
Unit-cell length c length_c	44.428 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	44.210 Å
R factor r_factor	0.2002
R_work r_work	0.1984
R_free r_free	0.2334

fit	/app/data/saxs_computation/c7/5c79/5c79.fit
pddf	/app/data/pr_computation/c7/5c79/5c79.pr.out
profile	/app/data/saxs_computation/c7/5c79/5c79.dat

PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2

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

Arf-GAP

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