1b4f

OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN

Method: X-RAY DIFFRACTION D_max: 125.7 Å Quality: REASONABLE

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

EPHB2

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 402–480 Chain B； UniProt 402–480 Chain C； UniProt 402–480 Chain D； UniProt 402–480	Fragment：SAM DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.95 Å R-free 0.273
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 402–480 Chain F； UniProt 402–480 Chain G； UniProt 402–480 Chain H； UniProt 402–480	Fragment：SAM DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.95 Å R-free 0.273

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 1B4F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F0M MONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) DOMAIN Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state 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
2QBX EphB2/SNEW Antagonistic Peptide Complex Deposited 2007-06-18	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 20–196（177 aa） Fragment：EphB2	Not recorded	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
2QBX EphB2/SNEW Antagonistic Peptide Complex Deposited 2007-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–196（177 aa） Fragment：EphB2	Not recorded	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
2QBX EphB2/SNEW Antagonistic Peptide Complex Deposited 2007-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–196（177 aa） Fragment：EphB2 Chain B 20–196（177 aa） Fragment：EphB2	Not recorded	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
3ZFM Crystal structure of EphB2 Deposited 2012-12-12	Different construct Different mutation/modification Different oligomeric state 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 5 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 4–82； UniProt 402–480 Author chain B； PDBConstruct 4–82； UniProt 402–480 Author chain C； PDBConstruct 4–82； UniProt 402–480 Author chain D； PDBConstruct 4–82； UniProt 402–480 Author chain E； PDBConstruct 4–82； UniProt 402–480 Author chain F； PDBConstruct 4–82； UniProt 402–480 Author chain G； PDBConstruct 4–82； UniProt 402–480 Author chain H； PDBConstruct 4–82； UniProt 402–480

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b4f
Deposition date deposition_date	1998-12-20
Structure title title	OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN
Keywords keywords	SAM DOMAIN, EPH RECEPTOR, SIGNAL TRANSDUCTION, OLIGOMER; SIGNAL TRANSDUCTION
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	36.97 Å
Radius of gyration Rg (electron density) rg_electron	37.05 Å
Forward intensity I(0) i0	75224500.00
Molecular weight molecular_weight	68145.0 kDa
Excluded volume excluded_volume	84929 Å³
Envelope volume envelope_volume	129520 Å³
Hydration-shell volume shell_volume	31530 Å³
Envelope diameter envelope_diameter	128.2 Å
Shell Rg shell_rg	39.56 Å
Envelope Rg envelope_rg	36.52 Å
Shape Rg shape_rg	37.08 Å
Total Rg total_rg	37.17 Å
Total atoms total_atoms	4762
Residues n_residues	599
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	125.7 Å
Rg (real space) rg_real	37.28 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	7.5220e+07
I(0) uncertainty (real space) i0_real_error	1.4800e+06
Rg (reciprocal space) rg_reciprocal	37.09 Å
I(0) (reciprocal space) i0_reciprocal	75210000.0000
Solution quality estimate total_estimate	0.6211
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.0 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.616
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5296000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.636; Smooth: 0.859

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1b4fa_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fb_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fc_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fd_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fe_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4ff_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fg_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

Domain ID domain_id	d1b4fh_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

CATH v4.4 (8 domains)

Domain ID domain_id	1b4fA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	1b4fH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

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8. Citations (1)

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Unit-cell length a length_a	73.897 Å
Unit-cell length b length_b	73.897 Å
Unit-cell length c length_c	104.547 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	32

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	26.000 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2730

Description description	EPHB2
Molecular weight formula_weight	9401.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	5564

OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN

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

EPHB2

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	685

fit	/app/data/saxs_computation/b4/1b4f/1b4f.fit
pddf	/app/data/pr_computation/b4/1b4f/1b4f.pr.out
profile	/app/data/saxs_computation/b4/1b4f/1b4f.dat