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2y6m

Crystal structure of EphA4 kinase domain

Method: X-RAY DIFFRACTION Dmax: 67.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EPHRIN TYPE-A RECEPTOR 4

MUS MUSCULUS

UniProt Q03137

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 606–896 Fragment：KINASE DOMAIN, RESIDUES 606-896 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：AMMONIUM SULFATE, BIS TRIS PH5.5, PEG 10 K Resolution 1.70 Å R-free 0.203

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 2Y6M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B0X THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MECHANISM FOR MODULAR DIMERIZATION. Deposited 1998-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 888–981（94 aa） Fragment：SAM DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.00 Å R-free 0.278
2XYU Crystal structure of EphA4 kinase domain in complex with VUF 12058 Deposited 2010-11-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 612–896（285 aa） Fragment：KINASE DOMAIN, RESIDUES 1548-1832
Not recorded GOL GLYCEROL × 6 Q9G 5-(5-FLUORO-2-METHYLPHENYL)-6,7,8,9-TETRAHYDRO-3H-PYRAZOLO[3,4-C]ISOQUINOLIN-1-AMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；AMMONIUM SULFATE, BISTRIS PH 5.5, PEG 10K
Resolution 2.12 Å R-free 0.230
2Y6O Crystal structure of EphA4 kinase domain in complex with Dasatinib. Deposited 2011-01-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 606–896（291 aa） Fragment：KINASE DOMAIN, RESIDUES 606-896
Not recorded 1N1 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；AMMONIUM SULFATE, BIS TRIS PH 5.5, PEG 10K
Resolution 1.54 Å R-free 0.201

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

View Construct and Data Evidence
UniProt name EPHA4_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–291； UniProt 606–896

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 2y6m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2y6m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2y6m
Deposition date deposition_date2011-01-25
Structure title titleCrystal structure of EphA4 kinase domain
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_guinier20.39 Å
Radius of gyration Rg (electron density) rg_electron19.53 Å
Forward intensity I(0) i014820200.00
Molecular weight molecular_weight29601.0 kDa
Excluded volume excluded_volume37335 ų
Envelope volume envelope_volume44263 ų
Hydration-shell volume shell_volume19181 ų
Envelope diameter envelope_diameter66.5 Å
Shell Rg shell_rg25.68 Å
Envelope Rg envelope_rg19.83 Å
Shape Rg shape_rg19.50 Å
Total Rg total_rg20.51 Å
Total atoms total_atoms2073
Residues n_residues262
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 dmax67.0 Å
Rg (real space) rg_real20.35 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real1.4820e+07
I(0) uncertainty (real space) i0_real_error1.7220e+05
Rg (reciprocal space) rg_reciprocal20.36 Å
I(0) (reciprocal space) i0_reciprocal14820000.0000
Solution quality estimate total_estimate0.6609
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.0 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0063
Highest regularization parameter α highest_alpha3982000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2y6ma_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id2y6mA01
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_id2y6mA02
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)