SAXSdb — 2lp0

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

Homeobox protein Hox-C9

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 192–251	Fragment：UNP residues 192-251	Geminin × 1 （O75496）	SOLUTION NMR NMR measurement conditions：pH 6.5；296 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-1, 1.0 mM Geminin-2, 25 mM potassium phosphate-3, 100 mM sodium chloride-4, 5 mM DTT-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.0 mM Hox-C9-6, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-7, 25 mM potassium phosphate-8, 100 mM sodium chloride-9, 5 mM DTT-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-11, 1.0 mM Geminin-12, 25 mM potassium phosphate-13, 100 mM sodium chloride-14, 5 mM DTT-15, 100% D2O \| 100% D2O NMR sample composition：1.0 mM Hox-C9-16, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-17, 25 mM potassium phosphate-18, 100 mM sodium chloride-19, 5 mM DTT-20, 100% D2O \| 100% D2O	Resolution not provided

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 2LP0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MSY Solution structure of Hox homeodomain Deposited 2014-08-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 184–251（68 aa） Fragment：UNP RESIDUES 184-251	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] MES-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	HXC9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 192–251

Geminin

Homo sapiens

UniProt O75496

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 171–190	Fragment：UNP residues 171-190	Homeobox protein Hox-C9 × 1 （P31274）	SOLUTION NMR NMR measurement conditions：pH 6.5；296 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-1, 1.0 mM Geminin-2, 25 mM potassium phosphate-3, 100 mM sodium chloride-4, 5 mM DTT-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.0 mM Hox-C9-6, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-7, 25 mM potassium phosphate-8, 100 mM sodium chloride-9, 5 mM DTT-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] Hox-C9-11, 1.0 mM Geminin-12, 25 mM potassium phosphate-13, 100 mM sodium chloride-14, 5 mM DTT-15, 100% D2O \| 100% D2O NMR sample composition：1.0 mM Hox-C9-16, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-17, 25 mM potassium phosphate-18, 100 mM sodium chloride-19, 5 mM DTT-20, 100% D2O \| 100% D2O	Resolution not provided

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 2LP0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T6F Crystal Structure of the Coiled-coil Dimerization Motif of Geminin Deposited 2004-05-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 109–145（37 aa） Fragment：COILED-COIL DOMAIN Chain B 109–145（37 aa） Fragment：COILED-COIL DOMAIN	Mutation：A1T Mutation：A1T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；10% PEG 6000, 5% MPD, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.47 Å R-free 0.221
1UII Crystal structure of Geminin coiled-coil domain Deposited 2003-07-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 70–152（83 aa） Fragment：coiled-coil domain Chain B 70–152（83 aa） Fragment：coiled-coil domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.36M Sodium Acetate, 0.1M TRIS, 30% PEG 4000, pH 8.5, EVAPORATION, temperature 293K	Resolution 2.00 Å R-free 0.239
2WVR Human Cdt1:Geminin complex Deposited 2009-10-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PH 7.5 100-150 MM NACL CAPILLARY GRADIENT	Resolution 3.30 Å R-free 0.301
4BRY The Idas:Geminin heterodimeric parallel coiled-coil Deposited 2013-06-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 83–160（78 aa） Fragment：COILED-COIL, RESIDUES 83-160	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M SPG PH 7.5, 10 % ISOPROPANOL	Resolution 2.89 Å R-free 0.226
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 195–209（15 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 195–209（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241

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

View Construct and Data Evidence

UniProt name	GEMI_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–20； UniProt 171–190

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	2lp0
Deposition date deposition_date	2012-01-29
Structure title title	The solution structure of homeodomain-protein complex
Keywords keywords	homeodomain, TRANSCRIPTION-CELL CYCLE complex; TRANSCRIPTION/CELL CYCLE
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.04 Å
Radius of gyration Rg (electron density) rg_electron	13.51 Å
Forward intensity I(0) i0	156790000.00
Molecular weight molecular_weight	100530.0 kDa
Excluded volume excluded_volume	124600 Å³
Envelope volume envelope_volume	32661 Å³
Hydration-shell volume shell_volume	16264 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	23.21 Å
Envelope Rg envelope_rg	17.54 Å
Shape Rg shape_rg	13.50 Å
Total Rg total_rg	14.01 Å
Total atoms total_atoms	14040
Residues n_residues	800
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	51.1 Å
Rg (real space) rg_real	14.05 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.5680e+08
I(0) uncertainty (real space) i0_real_error	1.6730e+06
Rg (reciprocal space) rg_reciprocal	14.05 Å
I(0) (reciprocal space) i0_reciprocal	156800000.0000
Solution quality estimate total_estimate	0.8359
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.018
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	314400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.990

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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	Homeobox protein Hox-C9
Molecular weight formula_weight	7739.2 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	14040

TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN

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	Geminin
Molecular weight formula_weight	2330.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NQEFDSEEETVEDSLVEDSE

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

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2lp0a_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

CATH v4.4 (1 domains)

Domain ID domain_id	2lp0A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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8. Citations (1)

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fit	/app/data/saxs_computation/lp/2lp0/2lp0.fit
pddf	/app/data/pr_computation/lp/2lp0/2lp0.pr.out
profile	/app/data/saxs_computation/lp/2lp0/2lp0.dat

The solution structure of homeodomain-protein complex

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

Homeobox protein Hox-C9

State in the Current Structure

Other States of the Same Protein in the Database

Geminin

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)