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- PDB-5hes: Human leucine zipper- and sterile alpha motif-containing kinase (... -

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Basic information

Entry
Database: PDB / ID: 5hes
TitleHuman leucine zipper- and sterile alpha motif-containing kinase (ZAK, MLT, HCCS-4, MRK, AZK, MLTK) in complex with vemurafenib
ComponentsMitogen-activated protein kinase kinase kinase MLT
KeywordsTRANSFERASE / Kinase / Complex
Function / homology
Function and homology information


positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / protein kinase regulator activity / stress-activated protein kinase signaling cascade ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / protein kinase regulator activity / stress-activated protein kinase signaling cascade / positive regulation of programmed cell death / limb development / regulation of mitotic metaphase/anaphase transition / embryonic digit morphogenesis / cellular response to UV-B / pyroptotic inflammatory response / p38MAPK cascade / MAP kinase kinase kinase activity / protein kinase activator activity / stress-activated MAPK cascade / JNK cascade / cytoskeleton organization / DNA damage checkpoint signaling / chromosome segregation / cellular response to gamma radiation / MAPK cascade / ribosome binding / protein autophosphorylation / small ribosomal subunit rRNA binding / cell differentiation / protein phosphorylation / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SAM domain (Sterile alpha motif) / : / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...SAM domain (Sterile alpha motif) / : / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / 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-032 / Mitogen-activated protein kinase kinase kinase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMathea, S. / Salah, E. / Abdul Azeez, K.R. / Tallant, C. / Szklarz, M. / Chaikuad, A. / Shrestha, B. / Sorrell, F.J. / Elkins, J.M. / Shrestha, L. ...Mathea, S. / Salah, E. / Abdul Azeez, K.R. / Tallant, C. / Szklarz, M. / Chaikuad, A. / Shrestha, B. / Sorrell, F.J. / Elkins, J.M. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib.
Authors: Mathea, S. / Abdul Azeez, K.R. / Salah, E. / Tallant, C. / Wolfreys, F. / Konietzny, R. / Fischer, R. / Lou, H.J. / Brennan, P.E. / Schnapp, G. / Pautsch, A. / Kessler, B.M. / Turk, B.E. / Knapp, S.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Oct 25, 2017Group: Structure summary / Item: _chem_comp.pdbx_synonyms
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase MLT
B: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5696
Polymers70,4652
Non-polymers1,1044
Water3,225179
1
A: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7843
Polymers35,2321
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase MLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7843
Polymers35,2321
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.712, 78.712, 133.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase MLT / Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif- ...Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif-containing kinase / MLK-like mitogen-activated protein triple kinase / Mixed lineage kinase-related kinase / MRK / Sterile alpha motif- and leucine zipper-containing kinase AZK


Mass: 35232.301 Da / Num. of mol.: 2 / Fragment: UNP residues 5-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAK, MLTK, HCCS4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-032 / N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide / Vemurafenib / PLX4032


Mass: 489.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H18ClF2N3O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM bis-tris-propane pH 6.5, 200 mM sodium malonate, 20% PEG3350, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→78.7 Å / Num. obs: 44222 / % possible obs: 99.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.1
Reflection shellResolution: 2.14→2.21 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3450 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.7refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTC

3dtc


Resolution: 2.14→78.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.226 --
Rwork0.18 --
obs-44222 99.6 %
Refinement stepCycle: LAST / Resolution: 2.14→78.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4526 0 74 179 4779

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