SAXSdb — 7d2g

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

Liprin-alpha-2

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 102–150 Chain B； UniProt 102–150	Fragment：UNP residues 102-150 Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.263
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 102–150 Chain D； UniProt 102–150	Fragment：UNP residues 102-150 Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.263

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 7D2G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TAC Crystal Structure of the Liprin-alpha/CASK complex Deposited 2011-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 866–1193（328 aa） Fragment：UNP residues 866-1193	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.4M ammonium sulfate, 0.2M NaCl, MES buffer, pH 6.5, vapor diffusion, hanging drop, temperature 289K	Resolution 2.20 Å R-free 0.236
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different mutation/modification 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 866–1193（328 aa） Fragment：UNP residues 866-975, 1113-1193	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different mutation/modification 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 866–1193（328 aa） Fragment：UNP residues 866-975, 1113-1193	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
6IUH Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 Deposited 2018-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 642–671（30 aa）	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267
6IUH Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 Deposited 2018-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 642–671（30 aa）	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267
7D2E Tetrameric coiled-coil structure of liprin-alpha2_H3 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 164–235（72 aa） Fragment：UNP residues 164-235 Chain B 164–235（72 aa） Fragment：UNP residues 164-235 Chain C 164–235（72 aa） Fragment：UNP residues 164-235 Chain D 164–235（72 aa） Fragment：UNP residues 164-235	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6,000	Resolution 1.70 Å R-free 0.269
7D2H Tetrameric coiled-coil structure of liprin-alpha2_H2 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 102–163（62 aa） Fragment：UNP residues 102-163 Chain B 102–163（62 aa） Fragment：UNP residues 102-163 Chain C 102–163（62 aa） Fragment：UNP residues 102-163 Chain D 102–163（62 aa） Fragment：UNP residues 102-163	Mutation：C143A Mutation：C143A Mutation：C143A Mutation：C143A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v Polyethylene glycol 8,000	Resolution 2.20 Å R-free 0.281
8Z22 Crystal structure of the liprin-alpha2/RIM1 complex Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 300–404（105 aa） Chain D 300–404（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；28% V/V 2-Propanol; 0.1M BIS-TRIS pH 6.5; 3% V/V Polyethylene glycol 200	Resolution 2.75 Å R-free 0.234

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

View Construct and Data Evidence

UniProt name	LIPA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–55； UniProt 102–150 Author chain B； PDBConstruct 7–55； UniProt 102–150 Author chain C； PDBConstruct 7–55； UniProt 102–150 Author chain D； PDBConstruct 7–55； UniProt 102–150

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	7d2g
Deposition date deposition_date	2020-09-16
Structure title title	Coiled-coil structure of liprin-alpha2_H2delC
Keywords keywords	Coiled-coil, 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	23.84 Å
Radius of gyration Rg (electron density) rg_electron	24.45 Å
Forward intensity I(0) i0	10495900.00
Molecular weight molecular_weight	23190.0 kDa
Excluded volume excluded_volume	28570 Å³
Envelope volume envelope_volume	38661 Å³
Hydration-shell volume shell_volume	15239 Å³
Envelope diameter envelope_diameter	98.5 Å
Shell Rg shell_rg	27.54 Å
Envelope Rg envelope_rg	25.52 Å
Shape Rg shape_rg	24.57 Å
Total Rg total_rg	24.54 Å
Total atoms total_atoms	1611
Residues n_residues	194
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	96.3 Å
Rg (real space) rg_real	24.38 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	1.0500e+07
I(0) uncertainty (real space) i0_real_error	1.5200e+05
Rg (reciprocal space) rg_reciprocal	24.25 Å
I(0) (reciprocal space) i0_reciprocal	10500000.0000
Solution quality estimate total_estimate	0.7047
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.803
Kurtosis Kurtosis kurtosis	0.332
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	893700.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.351; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.114; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Liprin-alpha-2
Molecular weight formula_weight	6453.1 kDa
Mutation mutation	L106M, C143A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1743

GPGSEFEFAAMTKELNACREQLLEKEEEISELKAERNNTRLLLEHLEALVSRHER

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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8. Citations (1)

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Unit-cell length a length_a	126.057 Å
Unit-cell length b length_b	33.410 Å
Unit-cell length c length_c	73.631 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2375
R_work r_work	0.2362
R_free r_free	0.2625

fit	/app/data/saxs_computation/d2/7d2g/7d2g.fit
pddf	/app/data/pr_computation/d2/7d2g/7d2g.pr.out
profile	/app/data/saxs_computation/d2/7d2g/7d2g.dat

Coiled-coil structure of liprin-alpha2_H2delC

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

Liprin-alpha-2

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