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- PDB-9n9x: Structure of HPK1 with C5 bound at its active site -

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Basic information

Entry
Database: PDB / ID: 9n9x
TitleStructure of HPK1 with C5 bound at its active site
ComponentsMitogen-activated protein kinase kinase kinase kinase 1
KeywordsTRANSFERASE/INHIBITOR / kinase / inhibitor / HDX / molecular dynamics / HX-ESP / 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 / protein autophosphorylation / cell population proliferation / protein phosphorylation / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / intracellular signal transduction ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / protein autophosphorylation / cell population proliferation / protein phosphorylation / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / intracellular signal transduction / 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 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / : / 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
: / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKiefer, J.R. / Wang, W. / Wu, P. / Walters, B.T. / Dou, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.
Authors: Walters, B.T. / Patapoff, A.W. / Kiefer, J.R. / Wu, P. / Wang, W.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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


Theoretical massNumber of molelcules
Total (without water)71,25610
Polymers70,0372
Non-polymers1,2198
Water2,000111
1
A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6285
Polymers35,0181
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6285
Polymers35,0181
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.120, 75.870, 86.060
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35018.434 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1BWL / (1R,2S)-2-cyanocyclopentyl [(6P)-8-amino-7-fluoro-6-(8-methyl-2,3-dihydro-1H-pyrido[2,3-b][1,4]oxazin-7-yl)isoquinolin-3-yl]carbamate


Mass: 462.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23FN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: not provided by author

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Data collection

DiffractionMean temperature: 91 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→44.5 Å / Num. obs: 25468 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.087 / Rrim(I) all: 0.158 / Χ2: 1.53 / Net I/σ(I): 8.9 / Num. measured all: 85274
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.639 / Num. measured all: 8579 / Num. unique obs: 2508 / CC1/2: 0.791 / Rpim(I) all: 0.405 / Rrim(I) all: 0.758 / Χ2: 1.05 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 21.757 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27615 1234 4.8 %RANDOM
Rwork0.22477 ---
obs0.22727 24210 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.053 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å2-0 Å23.18 Å2
2---2.72 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 86 111 4711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164526
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.6726382
X-RAY DIFFRACTIONr_angle_other_deg0.3271.59210408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.152527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05810801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8932.5432319
X-RAY DIFFRACTIONr_mcbond_other0.8932.5422318
X-RAY DIFFRACTIONr_mcangle_it1.4884.572897
X-RAY DIFFRACTIONr_mcangle_other1.4874.5712898
X-RAY DIFFRACTIONr_scbond_it0.9672.7182390
X-RAY DIFFRACTIONr_scbond_other0.9582.7172390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.664.943486
X-RAY DIFFRACTIONr_long_range_B_refined4.02125.945450
X-RAY DIFFRACTIONr_long_range_B_other4.0225.945451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 91 -
Rwork0.285 1790 -
obs--99 %
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)
14.29340.39931.39391.92620.41651.5804-0.14730.30980.6033-0.66890.0576-0.4751-0.33160.4830.08970.3131-0.05030.11690.23830.09570.5169-32.302979.576729.9306
22.64610.3471-1.11013.96350.60845.3571-0.00260.1540.3219-0.3495-0.168-0.1326-0.39140.12690.17060.06170.0118-0.00190.05820.00390.2219-49.459970.57135.616
32.5559-0.9167-0.20330.5787-0.35893.6817-0.0463-0.4853-0.3170.08370.1327-0.04670.52360.2096-0.08640.34520.04990.03240.23730.02950.3571-27.793127.549924.0573
43.0244-0.7793-0.57431.99570.04223.19570.0521-0.0215-0.0104-0.14960.0655-0.020.228-0.1199-0.11770.21090.01660.07880.0438-0.0360.1925-28.08835.57145.2196
51.167-0.4538-1.34852.38521.54582.04310.13530.10670.0269-0.26960.1373-0.5608-0.26310.0144-0.27270.21380.02430.07940.24840.03080.3314-39.561648.223824.8682
62.9072-0.4171-0.33882.9976-0.12042.68870.19550.30220.1918-0.4152-0.0919-0.0498-0.2384-0.1528-0.10360.27150.01080.08920.13810.02690.1784-29.440145.5807-1.3812
72.3572-1.9908-3.07422.39362.2924.14050.1288-0.11470.09470.418-0.0694-0.2464-0.40580.2052-0.05940.6107-0.00960.11370.24980.05940.3726-36.004458.214616.7639
81.4242-0.4158-0.31795.11910.54632.83770.07990.0936-0.1131-0.1702-0.17220.19240.2607-0.25480.09230.045-0.00250.01320.099-0.03220.1661-55.132559.989836.3271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 94
2X-RAY DIFFRACTION2A95 - 156
3X-RAY DIFFRACTION3B5 - 94
4X-RAY DIFFRACTION4B95 - 156
5X-RAY DIFFRACTION5B157 - 193
6X-RAY DIFFRACTION6B194 - 294
7X-RAY DIFFRACTION7A157 - 193
8X-RAY DIFFRACTION8A194 - 294

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