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3zfm

Crystal structure of EphB2

Method: X-RAY DIFFRACTION Dmax: 65.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EPHRIN TYPE-B RECEPTOR 2

HOMO SAPIENS

UniProt P29323

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 604–898 Fragment：KINASE DOMAIN, RESIDUES 604-898 No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.27 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 3ZFM 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 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 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 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 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 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

3 other PDB entries and 6 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 4–298； UniProt 604–898

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

SAXS profile for 3zfm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zfm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zfm
Deposition date deposition_date2012-12-12
Structure title titleCrystal structure of EphB2
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.05 Å
Radius of gyration Rg (electron density) rg_electron19.07 Å
Forward intensity I(0) i013615900.00
Molecular weight molecular_weight27560.0 kDa
Excluded volume excluded_volume34444 ų
Envelope volume envelope_volume41177 ų
Hydration-shell volume shell_volume18377 ų
Envelope diameter envelope_diameter63.7 Å
Shell Rg shell_rg25.14 Å
Envelope Rg envelope_rg19.40 Å
Shape Rg shape_rg19.06 Å
Total Rg total_rg20.01 Å
Total atoms total_atoms1933
Residues n_residues249
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.2 Å
Rg (real space) rg_real20.02 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real1.3620e+07
I(0) uncertainty (real space) i0_real_error1.8050e+05
Rg (reciprocal space) rg_reciprocal20.03 Å
I(0) (reciprocal space) i0_reciprocal13620000.0000
Solution quality estimate total_estimate0.8906
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.349
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3731000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.974
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3zfma_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3zfmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3zfmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)