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- PDB-8h59: A fungal MAP kinase in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8h59
TitleA fungal MAP kinase in complex with an inhibitor
ComponentsMitogen-activated protein kinase MPS1
KeywordsSIGNALING PROTEIN/INHIBITOR / kinase / fungal / SIGNALING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of mitotic cytokinesis / cell integrity MAPK cascade / positive regulation of developmental process / positive regulation of calcium ion import across plasma membrane / negative regulation of glucose mediated signaling pathway / MAP kinase activity / mitogen-activated protein kinase / positive regulation of calcium-mediated signaling / protein phosphorylation / protein serine kinase activity ...negative regulation of mitotic cytokinesis / cell integrity MAPK cascade / positive regulation of developmental process / positive regulation of calcium ion import across plasma membrane / negative regulation of glucose mediated signaling pathway / MAP kinase activity / mitogen-activated protein kinase / positive regulation of calcium-mediated signaling / protein phosphorylation / protein serine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-KR9 / Mitogen-activated protein kinase MPS1
Similarity search - Component
Biological speciesPyricularia oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKong, Z. / Zhang, X. / Wang, D. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mbio / Year: 2023
Title: Structure-Aided Identification of an Inhibitor Targets Mps1 for the Management of Plant-Pathogenic Fungi.
Authors: Kong, Z. / Zhang, X. / Zhou, F. / Tang, L. / Chen, Y. / Li, S. / Zhang, X. / Kuai, L. / Su, W. / Cui, W. / Cai, J. / Wang, Y. / Yang, J. / Peng, Y.L. / Wang, D. / Liu, J.
History
DepositionOct 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 10, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase MPS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7222
Polymers46,1581
Non-polymers5641
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17960 Å2
Unit cell
Length a, b, c (Å)75.040, 75.040, 159.058
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mitogen-activated protein kinase MPS1 / MAPK MPS1


Mass: 46158.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae 70-15 (fungus) / Strain: 70-15 / Gene: MPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: G4N374, mitogen-activated protein kinase
#2: Chemical ChemComp-KR9 / ~{N}-[(2~{S})-3-(1~{H}-indol-3-yl)-1-(methylamino)-1-oxidanylidene-propan-2-yl]-8-[2-methoxy-5-(trifluoromethyloxy)phenyl]-1,6-naphthyridine-2-carboxamide


Mass: 563.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H24F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20%% (v/v) Tacsimate, pH 6.0, 0.05 M sodium cacodylate trihydrate, pH 6.5, and 1.0 mM Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 29013 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 39.49 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.033 / Rrim(I) all: 0.146 / Χ2: 1.024 / Net I/σ(I): 3.9 / Num. measured all: 563437
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.15-2.1920.40.91414080.9150.2070.9370.437
2.19-2.2320.30.7814210.9270.1770.80.463
2.23-2.2720.10.6414210.9530.1450.6560.475
2.27-2.3219.90.58914330.9530.1350.6040.487
2.32-2.3719.60.49714060.9680.1150.510.494
2.37-2.4218.50.43914610.9770.1050.4520.532
2.42-2.4819.20.37613990.9780.0880.3860.551
2.48-2.55190.33214500.9820.0770.3410.622
2.55-2.6220.30.30114220.9870.0680.3080.648
2.62-2.7120.40.25714570.990.0580.2640.754
2.71-2.8120.30.23214130.9910.0530.2380.791
2.81-2.9220.10.20514420.9890.0470.210.892
2.92-3.0519.60.17714390.9920.0410.1821.053
3.05-3.2118.60.15514710.9940.0370.1591.263
3.21-3.4119.20.13814560.9950.0320.1421.476
3.41-3.6820.20.12714490.9960.0290.131.669
3.68-4.0519.60.11614620.9960.0270.121.89
4.05-4.63180.10614950.9960.0260.1092.013
4.63-5.8318.60.10715010.9960.0250.111.959
5.83-5017.10.09616070.9980.0240.0992.102

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z33

5z33


Resolution: 2.15→30.08 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 1394 4.93 %
Rwork0.1772 26866 -
obs0.1785 28260 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.46 Å2 / Biso mean: 52.714 Å2 / Biso min: 25.49 Å2
Refinement stepCycle: final / Resolution: 2.15→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 65 146 3234
Biso mean--39.84 48.34 -
Num. residues----375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.230.24691550.20182489264493
2.23-2.320.20341220.17842610273296
2.32-2.420.23551520.19352602275496
2.42-2.550.20381470.18412604275197
2.55-2.710.21161320.20452673280598
2.71-2.920.2391240.18852680280498
2.92-3.210.23761260.20372753287999
3.21-3.670.20741190.1752771289099
3.68-4.630.16821490.151927932942100
4.63-30.080.19691680.17252891305999
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)
10.560.3385-0.1020.39830.19990.51990.05020.7287-0.1131-0.3929-0.133-0.26690.18270.48710.00010.47050.07230.01070.6821-0.00440.46751.2166-34.988115.6731
20.9016-0.05840.9810.47930.14910.98710.12010.131-0.3279-0.2811-0.06760.31060.0192-0.01270.00030.36090.0275-0.0490.4436-0.05250.414843.0072-40.758124.1634
31.0603-0.34660.56710.569-0.43930.28970.07650.2116-0.0113-0.0633-0.0250.02850.14630.3009-0.00010.34630.0532-0.03230.4699-0.04340.377440.7398-36.068223.6348
41.38540.11310.05040.81620.08121.39450.0479-0.01820.11470.0680.04730.0398-0.09910.032-0.00010.19810.01640.00240.2995-0.0010.273451.9207-33.399838.9411
50.5628-0.14870.41030.07880.12870.76330.2697-0.1114-0.333-0.2108-0.11850.24480.376-0.01650.00010.37-0.0645-0.08970.41770.04610.571839.7599-49.954139.8998
60.1011-0.17960.12750.4657-0.5730.58840.0769-0.3364-0.01390.15550.0031-0.04910.0831-0.0085-00.28460.0176-0.02610.37660.0520.363651.8092-47.632447.4947
70.4262-0.4981-0.35770.50910.15480.24520.08950.1037-0.0062-0.3672-0.1347-0.33110.29770.46560.00090.43030.0609-0.06730.45810.04060.410562.1058-51.964248.4853
81.2425-1.03840.38470.769-0.48670.8393-0.1318-0.335-0.14940.47430.2920.13060.1358-0.2465-0.00010.4350.0063-0.00680.47950.05210.395855.6395-50.173158.0986
90.5053-0.75230.85620.5462-0.67181.1717-0.0316-0.36120.13130.1461-0.0340.31710.175-0.3744-0.00190.3320.01120.02350.4778-0.0270.40340.1221-35.739445.4437
100.4126-0.24110.00330.05920.61640.43560.12960.27890.10740.1713-0.2581-0.154-0.003-0.2933-0.0010.4204-0.0041-0.06520.41340.00620.38126.7441-22.902631.5921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 42 )A5 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 76 )A43 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 99 )A77 - 99
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 165 )A100 - 165
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 191 )A166 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 224 )A192 - 224
7X-RAY DIFFRACTION7chain 'A' and (resid 225 through 245 )A225 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 304 )A246 - 304
9X-RAY DIFFRACTION9chain 'A' and (resid 305 through 339 )A305 - 339
10X-RAY DIFFRACTION10chain 'A' and (resid 340 through 412 )A340 - 412

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