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Basic information

Entry
Database: PDB / ID: 3bpr
TitleCrystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor C52
ComponentsProto-oncogene tyrosine-protein kinase MER
KeywordsTRANSFERASE / ATP-BINDING / DISEASE MUTATION / GLYCOPROTEIN / KINASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / PROTO-ONCOGENE / RECEPTOR / RETINITIS PIGMENTOSA / SENSORY TRANSDUCTION / TYROSINE-PROTEIN KINASE / VISION / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Immunoglobulin domain / Membrane / Phosphoprotein / Polymorphism / Transmembrane
Function / homology
Function and homology information


negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / retina development in camera-type eye / cell-cell signaling / nervous system development / spermatogenesis / cell surface receptor signaling pathway / receptor complex / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / 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-OLP / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalker, J.R. / Huang, X. / Finerty Jr, P.J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structural insights into the inhibited states of the Mer receptor tyrosine kinase.
Authors: Huang, X. / Finerty, P. / Walker, J.R. / Butler-Cole, C. / Vedadi, M. / Schapira, M. / Parker, S.A. / Turk, B.E. / Thompson, D.A. / Dhe-Paganon, S.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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_conn / struct_ncs_dom_lim / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase MER
B: Proto-oncogene tyrosine-protein kinase MER
C: Proto-oncogene tyrosine-protein kinase MER
D: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,03911
Polymers143,5584
Non-polymers1,4817
Water2,360131
1
A: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2362
Polymers35,8891
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2593
Polymers35,8891
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2723
Polymers35,8891
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2723
Polymers35,8891
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.001, 91.702, 120.745
Angle α, β, γ (deg.)90.00, 94.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNAA575 - 86324 - 312
2LYSLYSBB576 - 86325 - 312
3ASNASNCC575 - 86324 - 312
4ASNASNDD575 - 86324 - 312

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Components

#1: Protein
Proto-oncogene tyrosine-protein kinase MER / C-mer / Receptor tyrosine kinase MerTK


Mass: 35889.434 Da / Num. of mol.: 4 / Fragment: Catalytic domain: Residues 574-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MERTK, MER / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12866, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-OLP / 2-(2-HYDROXYETHYLAMINO)-6-(3-CHLOROANILINO)-9-ISOPROPYLPURINE


Mass: 346.815 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H19ClN6O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 287 K / pH: 8.5
Details: Compound C52 (50 mM in DMSO) was added to 8 mg/ml MER protein to the final concentration of 2.5 mM. The mixture was rocked at 277 K overnight and further concentrated to about 35 mg/ml. ...Details: Compound C52 (50 mM in DMSO) was added to 8 mg/ml MER protein to the final concentration of 2.5 mM. The mixture was rocked at 277 K overnight and further concentrated to about 35 mg/ml. Crystals were grown by mixing 2 microliters of MER inhibitor solution and 2 microliters of reservoir solution (100 mM Tris-HCl pH 8.5, 3.64 M NaCl) at 287 K using the hanging-drop vapor-diffusion method. Crystals were cryo-protected with a solution composed of glycerol, ethylene glycol, glucose, and fructose., VAPOR DIFFUSION, HANGING DROP, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2007 / Details: MIRRORS
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 37537 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.15 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.53 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P0C

2p0c


Resolution: 2.8→47.3 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / SU B: 39.32 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R: 1.719 / ESU R Free: 0.42 / 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
Rfree0.30134 1889 5.1 %RANDOM
Rwork0.27361 ---
obs0.275 35338 98.73 %-
all-35338 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.487 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å21.07 Å2
2---4.73 Å20 Å2
3---9.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8073 0 99 131 8303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.98811451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64951039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02923.555346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.727151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4421553
X-RAY DIFFRACTIONr_chiral_restr0.080.21297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026244
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4935208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79448368
X-RAY DIFFRACTIONr_scbond_it1.26153396
X-RAY DIFFRACTIONr_scangle_it1.78773083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1932 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
1Atight thermal0.060.5
2Btight thermal0.070.5
3Ctight thermal0.070.5
4Dtight thermal0.060.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 128 -
Rwork0.348 2433 -
obs--92.76 %
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)
16.9281.9123-1.0290.5432-0.42921.5241-0.16051.22730.3015-0.59740.23870.55250.0432-0.1904-0.07810.4289-0.1082-0.16550.10480.07820.19778.734526.543146.125
24.1966-0.1788-1.30716.1192-0.77930.5212-0.19860.26660.0451-0.00570.1954-0.3494-0.33550.34820.00320.2-0.0558-0.0813-0.0793-0.0926-0.0313.596916.992755.3203
37.82390.735-0.23221.65461.573.5118-0.14870.09280.690.0052-0.0460.14880.2311-0.26830.19470.20570.0447-0.0272-0.1862-0.0108-0.0422-0.665415.015660.6221
44.37540.03180.2675.03050.47251.7731-0.19150.13050.0002-0.07530.04120.41610.1209-0.0690.15040.07780.00120.0232-0.11790.0269-0.0245-2.71764.169260.3569
53.7944-0.0831.97893.44961.13194.0447-0.17831.1959-0.4139-0.76830.3869-0.1429-0.35040.2649-0.20860.4215-0.15040.17070.096-0.03060.093717.5153-28.496245.8043
65.1698-2.6929-2.21410.00027.22668.0577-0.14770.15250.05950.08840.26850.11740.3582-0.4211-0.12080.1098-0.05950.1105-0.10330.1031-0.111813.0826-19.164256.772
77.725-0.0965-0.83472.3894-0.75142.328-0.07340.1228-0.1723-0.2239-0.0193-0.6850.3256-0.01490.09270.24180.01970.079-0.1861-0.0005-0.09226.7082-16.884759.8378
84.2713-0.22250.25725.933-0.2180.537-0.17660.04720.092-0.22410.0137-0.3998-0.00850.04010.16290.1370.01840.0189-0.0780.0027-0.146929.0485-6.434860.2619
93.30860.3806-0.71792.32450.67685.0719-0.1563-1.07230.3240.780.31-0.4710.04750.2051-0.15370.08910.1125-0.14510.1464-0.10940.284321.6033-36.609614.4901
101.65181.96950.17753.60870.39440.0456-0.2064-0.77820.02960.54350.48380.02582.086-0.7405-0.27740.03530.1138-0.08640.4391-0.07950.227818.8451-39.154615.6566
118.24261.5296-0.56174.2768-1.21921.6864-0.2970.13540.2665-0.10480.0814-0.0574-0.2162-0.11380.2157-0.1148-0.0096-0.0427-0.11260.0061-0.011524.6497-50.4095-1.7062
123.81690.3958-0.01836.5934-1.10821.3594-0.1301-0.1371-0.35330.1216-0.0413-0.3995-0.01590.12230.1714-0.197-0.01530.0075-0.0137-0.00610.072433.5446-59.0955-0.0534
133.85741.28871.90672.49591.30944.5402-0.06261.2187-0.4007-0.59310.4802-0.1721-0.08830.5453-0.41770.0667-0.12590.15160.1687-0.06590.437656.5488-45.9901-14.019
143.6191-0.59320.61699.50666.19096.157-0.23820.2239-0.2526-0.08310.13610.38360.2708-0.25960.1022-0.1321-0.0410.0923-0.02680.10190.143852.3149-36.3751-4.346
158.5072-0.1961-1.43133.6332-0.39072.7624-0.14260.1305-0.6734-0.06120.0229-0.06770.06650.3490.1197-0.08390.02960.056-0.06890.00250.012966.0837-34.25-0.2647
164.6315-0.6526-0.39476.208-1.1731.588-0.19130.14590.0674-0.0017-0.0009-0.3036-0.01780.07540.1922-0.2155-0.0405-0.0043-0.0209-0.04180.015368.4521-23.8130.1384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA575 - 65124 - 100
2X-RAY DIFFRACTION2AA652 - 695101 - 144
3X-RAY DIFFRACTION3AA696 - 730145 - 179
4X-RAY DIFFRACTION4AA731 - 863180 - 312
5X-RAY DIFFRACTION5BB576 - 65025 - 99
6X-RAY DIFFRACTION6BB651 - 695100 - 144
7X-RAY DIFFRACTION7BB696 - 730145 - 179
8X-RAY DIFFRACTION8BB731 - 863180 - 312
9X-RAY DIFFRACTION9CC575 - 65924 - 108
10X-RAY DIFFRACTION10CC661 - 674110 - 123
11X-RAY DIFFRACTION11CC675 - 731124 - 180
12X-RAY DIFFRACTION12CC732 - 863181 - 312
13X-RAY DIFFRACTION13DD575 - 65024 - 99
14X-RAY DIFFRACTION14DD651 - 695100 - 144
15X-RAY DIFFRACTION15DD696 - 730145 - 179
16X-RAY DIFFRACTION16DD731 - 863180 - 312

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