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- PDB-6cqf: Crystal structure of HPK1 in complex an inhibitor G1858 -

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Basic information

Entry
Database: PDB / ID: 6cqf
TitleCrystal structure of HPK1 in complex an inhibitor G1858
ComponentsMitogen-activated protein kinase kinase kinase kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-F97 / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.246 Å
AuthorsWu, P. / Lehoux, I. / Mortara, K. / Franke, Y. / Chan, B.K. / Wang, W.
CitationJournal: Structure / Year: 2019
Title: Hematopoietic Progenitor Kinase-1 Structure in a Domain-Swapped Dimer.
Authors: Wu, P. / Sneeringer, C.J. / Pitts, K.E. / Day, E.S. / Chan, B.K. / Wei, B. / Lehoux, I. / Mortara, K. / Li, H. / Wu, J. / Franke, Y. / Moffat, J.G. / Grogan, J.L. / Heffron, T.P. / Wang, W.
History
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5492
Polymers33,1201
Non-polymers4281
Water61334
1
A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules

A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0984
Polymers66,2412
Non-polymers8572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5160 Å2
ΔGint-39 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.868, 98.803, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 1 / HKP1 / Hematopoietic progenitor kinase / MAPK/ERK kinase kinase kinase 1 / MEKKK 1


Mass: 33120.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92918, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-F97 / N-{2-(3,3-difluoropyrrolidin-1-yl)-6-[(3R)-pyrrolidin-3-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-pyrazolo[4,3-c]pyridin-6-amine


Mass: 428.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26F2N8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.25 M sodium tartrate, 12% PEG8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 16438 / % possible obs: 96.4 % / Redundancy: 5.8 % / Net I/σ(I): 27.4
Reflection shellResolution: 2.25→2.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.246→33.639 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 765 4.67 %
Rwork0.2079 --
obs0.2101 16388 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.246→33.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 31 34 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052324
X-RAY DIFFRACTIONf_angle_d0.9543144
X-RAY DIFFRACTIONf_dihedral_angle_d13.056863
X-RAY DIFFRACTIONf_chiral_restr0.035347
X-RAY DIFFRACTIONf_plane_restr0.004392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2464-2.41980.39571230.31812656X-RAY DIFFRACTION83
2.4198-2.66320.31751500.29143143X-RAY DIFFRACTION98
2.6632-3.04840.30521580.24383235X-RAY DIFFRACTION100
3.0484-3.83980.30761780.22813221X-RAY DIFFRACTION100
3.8398-33.64310.20331560.17253368X-RAY DIFFRACTION99
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)
10.83580.02780.08531.2128-0.65640.35880.36140.0010.4808-0.3414-0.16950.3614-0.46370.31250.00070.795-0.0343-0.15570.52-0.01010.715-32.5196-1.2743-21.7804
20.75040.1651-0.24072.76570.31890.35110.02560.0692-0.03810.12110.075-0.14380.04260.08060.00010.44110.0369-0.01360.487-0.03210.4403-18.0183-16.6137-10.1525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 6:93
2X-RAY DIFFRACTION2chain A and resi 94:293

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