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- PDB-3dko: Complex between the kinase domain of human ephrin type-a receptor... -

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Basic information

Entry
Database: PDB / ID: 3dko
TitleComplex between the kinase domain of human ephrin type-a receptor 7 (epha7) and inhibitor alw-ii-49-7
ComponentsEphrin type-A receptor 7
KeywordsTRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / ALTERNATIVE SPLICING / GLYCOPROTEIN / INHIBITOR / STRUCTURAL GENOMICS CONSORTIUM / SGC / Membrane / Phosphoprotein / Polymorphism / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


regulation of protein autophosphorylation / : / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / chemorepellent activity ...regulation of protein autophosphorylation / : / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / chemorepellent activity / EPH-Ephrin signaling / regulation of postsynapse organization / negative chemotaxis / retinal ganglion cell axon guidance / EPHA-mediated growth cone collapse / regulation of cell-cell adhesion / growth factor binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / phosphorylation / regulation of peptidyl-tyrosine phosphorylation / regulation of ERK1 and ERK2 cascade / axon guidance / modulation of chemical synaptic transmission / brain development / receptor protein-tyrosine kinase / positive regulation of neuron apoptotic process / protein tyrosine kinase activity / neuron apoptotic process / positive regulation of protein phosphorylation / glutamatergic synapse / dendrite / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 7, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain ...Ephrin type-A receptor 7, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-IHZ / Ephrin type-A receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWalker, J.R. / Syeda, F. / Gray, N. / Butler-Cole, C. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Kinase domain of human ephrin type-a receptor 7 (epha7) in complex with ALW-II-49-7
Authors: Walker, J.R. / Syeda, F. / Gray, N. / Butler-Cole, C. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJun 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6542
Polymers36,2401
Non-polymers4141
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.658, 52.658, 217.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ephrin type-A receptor 7 / Tyrosine-protein kinase receptor EHK-3 / EPH homology kinase 3 / Receptor protein-tyrosine kinase HEK11


Mass: 36239.527 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 590-899
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BRAIN / Gene: EPHA7, EHK3, HEK11 / Plasmid: PNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q15375, receptor protein-tyrosine kinase
#2: Chemical ChemComp-IHZ / 5-[(2-methyl-5-{[3-(trifluoromethyl)phenyl]carbamoyl}phenyl)amino]pyridine-3-carboxamide


Mass: 414.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F3N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP ...Details: WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO WHICH MPD WAS ADDED TO 25%, , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 21903 / Num. obs: 21903 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.067 / Net I/σ(I): 38.92
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.19 / Num. unique all: 2253 / Rsym value: 0.417 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2REI

2rei


Resolution: 2→23.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.289 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 1062 4.9 %RANDOM
Rwork0.18917 ---
obs0.19118 20747 95.3 %-
all-21809 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.811 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2→23.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 30 156 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222254
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9633057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22223.529102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5311517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021733
X-RAY DIFFRACTIONr_nbd_refined0.1950.21067
X-RAY DIFFRACTIONr_nbtor_refined0.30.21562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.214
X-RAY DIFFRACTIONr_mcbond_it0.5991.51433
X-RAY DIFFRACTIONr_mcangle_it0.93922223
X-RAY DIFFRACTIONr_scbond_it1.4513961
X-RAY DIFFRACTIONr_scangle_it2.3294.5834
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 93 -
Rwork0.212 1549 -
obs--97.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
152.3212-10.26193.046816.7594-4.19771.2027-1.3328-3.8486-0.82841.63781.43362.3378-0.8689-0.259-0.10080.58220.29760.27990.398-0.01780.3728-23.504915.8956.7817
25.6051-4.31266.415915.8154-12.078329.9614-0.0209-0.13160.15121.03720.2688-0.1928-0.10920.3311-0.24790.21770.07510.0634-0.0546-0.04420.1554-24.550623.3388-2.2199
33.5596-1.44-1.727215.33523.310111.4513-0.07980.2148-0.22420.3223-0.06150.41560.8852-0.12970.14130.21310.0652-0.00640.01830.03340.1242-26.348116.8901-19.0731
46.3916-2.60590.89891.082-0.07214.5529-0.1467-0.2665-0.16070.1439-0.0111-0.01560.3753-0.37530.15790.3580.02440.07120.0023-0.01420.1223-24.138415.7756-8.054
50.9278-1.02160.09871.73820.05680.05510.17140.10040.0465-0.1808-0.0892-0.0147-0.1583-0.0306-0.08220.21730.01490.0310.10420.00660.1338-12.54877.8593-11.7383
60.98160.3196-0.60642.32330.2682.44540.0660.0866-0.07680.0556-0.07290.08150.1043-0.21410.00690.13430.00060.00590.1158-0.00280.1558-11.9762-5.2213-4.536
71.34030.0946-0.19553.86040.68723.6522-0.0602-0.0963-0.1140.22180.0203-0.2590.20270.21730.040.11360.0216-0.01910.0881-0.00760.1843-2.4782-7.6459-2.1622
815.6746-2.679216.037596.0936-32.01525.3694-2.0645-2.919-1.98972.72164.9309-4.0892-1.1194-0.8358-2.86640.52960.09080.150.6858-0.18460.468111.407-0.3139-12.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA607 - 61819 - 30
2X-RAY DIFFRACTION2AA619 - 62831 - 40
3X-RAY DIFFRACTION3AA629 - 65441 - 66
4X-RAY DIFFRACTION4AA655 - 69667 - 108
5X-RAY DIFFRACTION5AA697 - 770109 - 182
6X-RAY DIFFRACTION6AA771 - 841183 - 253
7X-RAY DIFFRACTION7AA842 - 893254 - 305
8X-RAY DIFFRACTION8AA894 - 902306 - 314

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