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- PDB-4zp5: MAP4K4 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4zp5
TitleMAP4K4 in complex with inhibitor
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTRANSFERASE/INHIBITOR / kinase / inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[5-(4-chlorophenyl)-1,3-oxazol-2-yl]benzamide / Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLiu, S.
CitationJournal: To Be Published
Title: Structure of MAP4K4 complex
Authors: Liu, S.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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 4
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8823
Polymers70,5832
Non-polymers2991
Water2,864159
1
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5902
Polymers35,2921
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)35,2921
Polymers35,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.633, 91.386, 97.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 4 / HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEKKK 4 / Nck-interacting kinase


Mass: 35291.508 Da / Num. of mol.: 2 / Fragment: UNP residues 1-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK / Production host: Simulium sp. iridescent virus
References: UniProt: O95819, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4QG / 4-[5-(4-chlorophenyl)-1,3-oxazol-2-yl]benzamide


Mass: 298.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClN2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→97.53 Å / Num. obs: 31533 / % possible obs: 94.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.67 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.3
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / % possible all: 67.1

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→66.69 Å / Cor.coef. Fo:Fc: 0.9295 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.348 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1588 5.07 %RANDOM
Rwork0.2291 ---
obs0.2309 31343 94.66 %-
Displacement parametersBiso mean: 60.05 Å2
Baniso -1Baniso -2Baniso -3
1-7.0536 Å20 Å20 Å2
2---3.0131 Å20 Å2
3----4.0405 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: 1 / Resolution: 2.29→66.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 21 159 4886
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084842HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.096553HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes121HARMONIC2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4842HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion19.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion621SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5429SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.37 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.328 79 4.7 %
Rwork0.2905 1601 -
all0.2924 1680 -
obs--94.66 %
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)
10.87970.65510.37193.52771.54881.9118-0.01230.0110.1041-0.0047-0.07750.2256-0.2544-0.02930.0898-0.18210.00890.0451-0.20370.0138-0.136373.480846.090711.3491
22.2494-0.3938-0.86961.15840.16622.44520.0376-0.21760.25040.2170.0879-0.1944-0.28840.4489-0.1255-0.1271-0.085-0.0596-0.134-0.0565-0.1318101.32232.705822.2977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|14 - A|173 A|186 - A|309 A|400 - A|400 }
2X-RAY DIFFRACTION2{ B|10 - B|161 B|163 - B|309 }

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