SAXSdb — 5lx2

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

KLTH0G14146p

Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–253	Not recorded	Phosphatidylinositol 4-kinase beta × 2 （A0A0B4J1S8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；MES, PEG 8000, ethylene glycol	Resolution 2.58 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 5LX2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LVZ Crystal structure of yeast 14-3-3 protein from Lachancea thermotolerans Deposited 2016-09-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–253（253 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；13% PEG 3350, 190 mM CaCl2, 3% glycerol	Resolution 1.95 Å R-free 0.223

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C5DN49_LACTC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 1–253

Phosphatidylinositol 4-kinase beta

OrganismNot specified

UniProt A0A0B4J1S8

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 304–309	Fragment：UNP residues 304-309 Non-standard monomer：Yes (specific site not provided by mmCIF)	KLTH0G14146p × 2 （C5DN49）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；MES, PEG 8000, ethylene glycol	Resolution 2.58 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 5LX2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N73 Solution structure of the ACBD3:PI4KB complex Deposited 2015-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 5–80（76 aa） Fragment：UNP residues 5-80	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.47 mM [U-13C; U-15N] protein_1, 0.47 mM [U-13C; U-15N] protein_2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8Q6F HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 4) Deposited 2023-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 531–828（298 aa）	Mutation：R409Q,R412Q	KHR 3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-2,5-dimethyl-7-(pyridin-4-ylmethylamino)pyrazolo[1,5-a]pyrimidine × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Sodium Formate	Resolution 1.51 Å R-free 0.224
8Q6G HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 8) Deposited 2023-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 531–828（298 aa）	Mutation：R409Q,R412Q	KIH 3-(3,4-dimethoxyphenyl)-7-[(4-fluorosulfonyloxyphenyl)methylamino]-2,5-dimethyl-pyrazolo[1,5-a]pyrimidine × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Sodium Formate	Resolution 1.54 Å R-free 0.221
8Q6H HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 11) Deposited 2023-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 531–828（298 aa）	Mutation：R409Q,R412Q	MG MAGNESIUM ION × 1 KI7 3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-7-[(4-fluorosulfonyloxyphenyl)methylamino]-2,5-dimethyl-pyrazolo[1,5-a]pyrimidine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Sodium Formate	Resolution 1.94 Å R-free 0.237

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0B4J1S8_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–6； UniProt 304–309

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	5lx2
Deposition date deposition_date	2016-09-19
Structure title title	Lt 14-3-3 in complex with PI4KIIIB peptide
Keywords keywords	phosphoserin, kinase, regulation, transferase; TRANSFERASE
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	19.95 Å
Radius of gyration Rg (electron density) rg_electron	18.90 Å
Forward intensity I(0) i0	13649300.00
Molecular weight molecular_weight	26998.0 kDa
Excluded volume excluded_volume	33539 Å³
Envelope volume envelope_volume	39216 Å³
Hydration-shell volume shell_volume	17761 Å³
Envelope diameter envelope_diameter	67.9 Å
Shell Rg shell_rg	24.92 Å
Envelope Rg envelope_rg	19.30 Å
Shape Rg shape_rg	18.90 Å
Total Rg total_rg	19.80 Å
Total atoms total_atoms	1897
Residues n_residues	240
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	66.8 Å
Rg (real space) rg_real	19.91 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.3650e+07
I(0) uncertainty (real space) i0_real_error	1.5870e+05
Rg (reciprocal space) rg_reciprocal	19.92 Å
I(0) (reciprocal space) i0_reciprocal	13650000.0000
Solution quality estimate total_estimate	0.8059
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.315
Kurtosis Kurtosis kurtosis	-0.216
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2430000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

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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	KLTH0G14146p
Molecular weight formula_weight	28603.9 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	1927

MSQSREDSVYLAKLAEQAERYEEMVDSMKAVASSGQELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEEAKDKSEHQVKLIRDYRSKIETELTKICDDILSVLDTHLIPSATTGESKVFYYKMKGDYHRYLAEFSSGEVRDKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSEAGQDEQQPAEGAQE

来源 Source

来源生物 organism	Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)
通用名 common_name	Yeast
NCBI Class编号 ncbi_taxonomy_id	559295
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Phosphatidylinositol 4-kinase beta
Molecular weight formula_weight	697.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TASNPK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5lx2A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

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8. Citations (1)

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Unit-cell length a length_a	64.063 Å
Unit-cell length b length_b	123.671 Å
Unit-cell length c length_c	38.688 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.579 Å
Low-resolution limit resolution_low	44.491 Å
R factor r_factor	0.2057
R_work r_work	0.2027
R_free r_free	0.2627

fit	/app/data/saxs_computation/lx/5lx2/5lx2.fit
pddf	/app/data/pr_computation/lx/5lx2/5lx2.pr.out
profile	/app/data/saxs_computation/lx/5lx2/5lx2.dat

Lt 14-3-3 in complex with PI4KIIIB peptide

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

KLTH0G14146p

State in the Current Structure

Other States of the Same Protein in the Database

Phosphatidylinositol 4-kinase beta

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)