SAXSdb — 6n8p

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

Lethal(2) giant larvae protein homolog 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 13–978	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；19.8 % PEG 3350, 0.29 M Na2SO4, 0.1 M bis-tris propane pH 7.5, 3% methanol	Resolution 3.19 Å R-free 0.250

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 6N8P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WP0 Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide Deposited 2014-01-08	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 640–654（15 aa） Fragment：UNP residues 640-654	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.2M lithium chloride, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.04 Å R-free 0.202
3WP1 Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl Deposited 2014-01-08	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 646–657（12 aa） Fragment：UNP residues 646-657	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.268
6N8Q Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 2. Deposited 2018-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13–978（966 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295.15 K；18-21 % PEG 2000 MME, 80-100 mM SPG pH 6.0	Resolution 2.20 Å R-free 0.226
6N8R Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 2. Deposited 2018-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13–978（966 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；25% PEG 1500, 100 mM SPG pH 8.0	Resolution 1.91 Å R-free 0.219
6N8S Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 3. Deposited 2018-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13–978（966 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；1.4 M ammonium sulfate, 100 mM Hepes pH 7.5, 150 mM NaCl, 1.07% 1,6-hexanediol	Resolution 3.90 Å R-free 0.298
6N8S Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 3. Deposited 2018-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 13–978（966 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；1.4 M ammonium sulfate, 100 mM Hepes pH 7.5, 150 mM NaCl, 1.07% 1,6-hexanediol	Resolution 3.90 Å R-free 0.298
8R3X Crystal structure of aPKC Iota kinase domain with LLGL2 peptide Deposited 2023-11-10	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 C 641–660（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；Morpheus Condition: 25% (v/v) MPD, 25% (v/v) PEG 1000, 25% (v/v) PEG 3350, 0.3 M NaNO3, 0.3 M Na2HPO4, 0.3 M (NH4)2SO4, 0.1 M MES/imidazole pH 6.5	Resolution 2.59 Å R-free 0.269
8R3X Crystal structure of aPKC Iota kinase domain with LLGL2 peptide Deposited 2023-11-10	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 D 641–660（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；Morpheus Condition: 25% (v/v) MPD, 25% (v/v) PEG 1000, 25% (v/v) PEG 3350, 0.3 M NaNO3, 0.3 M Na2HPO4, 0.3 M (NH4)2SO4, 0.1 M MES/imidazole pH 6.5	Resolution 2.59 Å R-free 0.269
9EJK Lgl2 bound to the aPKCiota-Par6b complex in nucleotide-free form. Head sub-complex region subtracted Deposited 2024-11-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 13–978（966 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9EJL Lgl2 bound to the aPKCiota-Par6B complex in nucleotide-free form. Conformation with visible head sub-complex. Deposited 2024-11-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 13–978（966 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.48 Å
9EJM Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form Deposited 2024-11-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 13–978（966 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å

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

View Construct and Data Evidence

UniProt name	L2GL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–967； UniProt 13–978

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	6n8p
Deposition date deposition_date	2018-11-30
Structure title title	Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 1.
Keywords keywords	Lgl, Polarity, beta propeller, LIPID BINDING PROTEIN; LIPID BINDING 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	32.83 Å
Radius of gyration Rg (electron density) rg_electron	32.28 Å
Forward intensity I(0) i0	128016000.00
Molecular weight molecular_weight	91341.0 kDa
Excluded volume excluded_volume	114770 Å³
Envelope volume envelope_volume	145520 Å³
Hydration-shell volume shell_volume	38522 Å³
Envelope diameter envelope_diameter	115.9 Å
Shell Rg shell_rg	38.24 Å
Envelope Rg envelope_rg	32.09 Å
Shape Rg shape_rg	32.28 Å
Total Rg total_rg	32.79 Å
Total atoms total_atoms	6453
Residues n_residues	827
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	109.6 Å
Rg (real space) rg_real	33.02 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.2800e+08
I(0) uncertainty (real space) i0_real_error	2.1140e+06
Rg (reciprocal space) rg_reciprocal	32.95 Å
I(0) (reciprocal space) i0_reciprocal	128000000.0000
Solution quality estimate total_estimate	0.8533
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.476
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36190000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.827

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lethal(2) giant larvae protein homolog 2
Molecular weight formula_weight	109275.1 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	6453

MRERLKRDLFQFNKTVEHGFPHQPSALGYSPSLRILAIGTRSGAIKLYGAPGVEFMGLHQENNAVTQIHLLPGQCQLVTLLDDNSLHLWSLKVKGGASELQEDESFTLRGPPGAAPSATQITVVLPHSSCELLYLGTESGNVFVVQLPAFRALEDRTISSDAVLQRLPEEARHRRVFEMVEALQEHPRDPNQILIGYSRGLVVIWDLQGSRVLYHFLSSQQLENIWWQRDGRLLVSCHSDGSYCQWPVSSEAQQPEPLRSLVPYGPFPCKAITRILWLTTRQGLPFTIFQGGMPRASYGDRHCISVIHDGQQTAFDFTSRVIGFTVLTEADPAATFDDPYALVVLAEEELVVIDLQTAGWPPVQLPYLASLHCSAITCSHHVSNIPLKLWERIIAAGSRQNAHFSTMEWPIDGGTSLTPAPPQRDLLLTGHEDGTVRFWDASGVCLRLLYKLSTVRVFLTDTDPNENFSAQGEDEWPPLRKVGSFDPYSDDPRLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLALEGPLSRVKSLKKSLRQSFRRMRRSRVSSRKRHPAGPPGEAQEGSAKAERPGLQNMELAPVQRKIEARSAEDSFTGFVRTLYFADTYLKDSSRHCPSLWAGTNGGTIYAFSLRVPPAERRMDEPVRAEQAKEIQLMHRAPVVGILVLDGHSVPLPEPLEVAHDLSKSPDMQGSHQLLVVSEEQFKVFTLPKVSAKLKLKLTALEGSRVRRVSVAHFGSRRAEDYGEHHLAVLTNLGDIQVVSLPLLKPQVRYSCIRREDVSGIASCVFTKYGQGFYLISPSEFERFSLSTKWLVEPRCLVDSAETKNHRPGNGAGPKKAPSRARNSGTQSDGEEKQPGLVMEREFTTASENLYFQ

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6n8pA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	78.699 Å
Unit-cell length b length_b	118.489 Å
Unit-cell length c length_c	126.639 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.193 Å
Low-resolution limit resolution_low	39.349 Å
R factor r_factor	0.2081
R_work r_work	0.2036
R_free r_free	0.2497

fit	/app/data/saxs_computation/n8/6n8p/6n8p.fit
pddf	/app/data/pr_computation/n8/6n8p/6n8p.pr.out
profile	/app/data/saxs_computation/n8/6n8p/6n8p.dat

Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 1.

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

Lethal(2) giant larvae protein homolog 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