SAXSdb — 2qbx

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

Ephrin type-B receptor 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 20–196	Fragment：EphB2	antagonistic peptide × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；100 mM Hepes, pH 7.2, 100 mM ammonium sulfate, and 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.270
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 20–196	Fragment：EphB2	antagonistic peptide × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；100 mM Hepes, pH 7.2, 100 mM ammonium sulfate, and 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.270
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 20–196 Chain B； UniProt 20–196	Fragment：EphB2	antagonistic peptide × 2 SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；100 mM Hepes, pH 7.2, 100 mM ammonium sulfate, and 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.270

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 2QBX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4F OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN Deposited 1998-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 402–480（79 aa） Fragment：SAM DOMAIN Chain B 402–480（79 aa） Fragment：SAM DOMAIN Chain C 402–480（79 aa） Fragment：SAM DOMAIN Chain D 402–480（79 aa） Fragment：SAM DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.95 Å R-free 0.273
1B4F OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN Deposited 1998-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 402–480（79 aa） Fragment：SAM DOMAIN Chain F 402–480（79 aa） Fragment：SAM DOMAIN Chain G 402–480（79 aa） Fragment：SAM DOMAIN Chain H 402–480（79 aa） Fragment：SAM DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.95 Å R-free 0.273
1F0M MONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) DOMAIN Deposited 2000-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 889–970（82 aa） Fragment：EPHB2 RECEPTOR FRAGMENT, SAM DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% peg, 70 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 25K	Resolution 2.20 Å R-free 0.264
3ZFM Crystal structure of EphB2 Deposited 2012-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 604–898（295 aa） Fragment：KINASE DOMAIN, RESIDUES 604-898	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.27 Å R-free 0.263

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

View Construct and Data Evidence

UniProt name	EPHB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 32–208； UniProt 20–196 Author chain B； PDBConstruct 32–208； UniProt 20–196

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	2qbx
Deposition date deposition_date	2007-06-18
Structure title title	EphB2/SNEW Antagonistic Peptide Complex
Keywords keywords	;Receptor tyrosine kinase, bi-directional signaling, tumorigenesis, angiogenesis, SIGNALING PROTEIN, Structural Genomics, PSI-2, Protein Structure Initiative, Accelerated Technologies Center for Gene to 3D Structure, ATCG3D ;; SIGNALING 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	28.44 Å
Radius of gyration Rg (electron density) rg_electron	28.08 Å
Forward intensity I(0) i0	34827400.00
Molecular weight molecular_weight	43457.0 kDa
Excluded volume excluded_volume	53173 Å³
Envelope volume envelope_volume	65845 Å³
Hydration-shell volume shell_volume	21406 Å³
Envelope diameter envelope_diameter	100.7 Å
Shell Rg shell_rg	32.45 Å
Envelope Rg envelope_rg	28.33 Å
Shape Rg shape_rg	27.98 Å
Total Rg total_rg	28.79 Å
Total atoms total_atoms	3039
Residues n_residues	372
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	97.5 Å
Rg (real space) rg_real	28.89 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	3.4830e+07
I(0) uncertainty (real space) i0_real_error	4.9760e+05
Rg (reciprocal space) rg_reciprocal	28.76 Å
I(0) (reciprocal space) i0_reciprocal	34820000.0000
Solution quality estimate total_estimate	0.7680
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.551
Kurtosis Kurtosis kurtosis	-0.524
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9045000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.546; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.417; Smooth: 0.927

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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	Ephrin type-B receptor 2
Molecular weight formula_weight	23664.7 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3222

MVSAIVLYVLLAAAAHSAFAAMVHHHHHHSAEETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNVFESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDSATKTFPNWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRSGFYLAFQDYGGCMSLIAVRVFYRK

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 polymer

Description description	antagonistic peptide
Molecular weight formula_weight	1506.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,P

SNEWIQPRLPQH

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2qbxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2qbxB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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8. Citations (1)

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Unit-cell length a length_a	40.183 Å
Unit-cell length b length_b	40.183 Å
Unit-cell length c length_c	235.025 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	34.790 Å
R factor r_factor	0.1979
R_work r_work	0.1942
R_free r_free	0.2695

fit	/app/data/saxs_computation/qb/2qbx/2qbx.fit
pddf	/app/data/pr_computation/qb/2qbx/2qbx.pr.out
profile	/app/data/saxs_computation/qb/2qbx/2qbx.dat

EphB2/SNEW Antagonistic Peptide Complex

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

Ephrin type-B receptor 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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)