SAXSdb — 6lbm

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

Forkhead box protein C2

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 72–172	Not recorded	IRE0 × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；50 mM HEPES, pH 7.5, 8%-12% PEG4000 (w/v), 250 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.	Resolution 2.84 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 6LBM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5V SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSCRIPTION FACTOR FREAC-11 (S12) Deposited 1999-10-12	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 69–162（94 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；300 K；Ionic strength (raw mmCIF value) 15 mM；Pressure AMBIENT NMR sample composition 1 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT NMR sample composition 1 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT	Resolution not provided
6AKO Crystal Structure of FOXC2 DBD Bound to DBE2 DNA Deposited 2018-09-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 72–172（101 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50 mM Bis-Tris propane (pH 6.68), 14% PEG4K, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP	Resolution 2.40 Å R-free 0.250
6AKP Crystal Structural of FOXC2 DNA binding domain bound to PC promoter Deposited 2018-09-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 72–172（101 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50mM NaOAc pH4.7, 14%PEG4K, 200mM NaCl, 10mM MgCl2, 0.5mM TCEP	Resolution 2.32 Å R-free 0.247
6O3T Structural basis of FOXC2 and DNA interactions Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 70–164（95 aa） Chain B 70–164（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298.15 K；30% PEG MME 2000, 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 10 mM BME	Resolution 3.06 Å R-free 0.268
9VRQ Crystal structure of FOXC2/NFAT1 complex bound to ARRE2 DNA Deposited 2025-07-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 72–172（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM MES 5.93, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP and 12-15% PEG 4K (w/v)	Resolution 2.80 Å R-free 0.288

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FOXC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 3–103； UniProt 72–172

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	6lbm
Deposition date deposition_date	2019-11-14
Structure title title	Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence
Keywords keywords	Forkhead transcription, DNA binding specificity, TRANSCRIPTION; TRANSCRIPTION
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	17.42 Å
Radius of gyration Rg (electron density) rg_electron	16.26 Å
Forward intensity I(0) i0	11862800.00
Molecular weight molecular_weight	20103.0 kDa
Excluded volume excluded_volume	22698 Å³
Envelope volume envelope_volume	28838 Å³
Hydration-shell volume shell_volume	15061 Å³
Envelope diameter envelope_diameter	58.6 Å
Shell Rg shell_rg	22.00 Å
Envelope Rg envelope_rg	16.59 Å
Shape Rg shape_rg	16.18 Å
Total Rg total_rg	17.22 Å
Total atoms total_atoms	1381
Residues n_residues	124
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	57.0 Å
Rg (real space) rg_real	17.32 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.1860e+07
I(0) uncertainty (real space) i0_real_error	1.5530e+05
Rg (reciprocal space) rg_reciprocal	17.33 Å
I(0) (reciprocal space) i0_reciprocal	11860000.0000
Solution quality estimate total_estimate	0.8078
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.362
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1561000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.995; 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	Forkhead box protein C2
Molecular weight formula_weight	12330.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	1393

GPKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFLRRRRRFKKKD

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 2 Entity 2 polymer

Description description	IRE0
Molecular weight formula_weight	6133.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,B

GGTGTAAACATGTTTACACC

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	12

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6lbmc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.14 — Forkhead DNA-binding domain

Domain ID domain_id	d6lbmc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	96.521 Å
Unit-cell length b length_b	42.656 Å
Unit-cell length c length_c	103.277 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.841 Å
Low-resolution limit resolution_low	39.281 Å
R factor r_factor	0.2340
R_work r_work	0.2327
R_free r_free	0.2626

fit	/app/data/saxs_computation/lb/6lbm/6lbm.fit
pddf	/app/data/pr_computation/lb/6lbm/6lbm.pr.out
profile	/app/data/saxs_computation/lb/6lbm/6lbm.dat

Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence

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

Forkhead box protein C2

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

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)