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- PDB-6hvd: Human SLK bound to a maleimide inhibitor -

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Basic information

Entry
Database: PDB / ID: 6hvd
TitleHuman SLK bound to a maleimide inhibitor
ComponentsSTE20-like serine/threonine-protein kinase
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase ...regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Polo kinase kinase / Polo kinase kinase / UVR domain / UVR 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. ...Polo kinase kinase / Polo kinase kinase / UVR domain / UVR 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
Chem-GUQ / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsSorrell, F.J. / Berger, B.T. / Salah, E. / Serafim, R.A.M. / Savitsky, P.A. / Krojer, T. / Bailey, H.J. / Pinkas, D. / Burgess-Brown, N.A. / von Delft, F. ...Sorrell, F.J. / Berger, B.T. / Salah, E. / Serafim, R.A.M. / Savitsky, P.A. / Krojer, T. / Bailey, H.J. / Pinkas, D. / Burgess-Brown, N.A. / von Delft, F. / Knapp, S. / Arrowsmith, C. / Bountra, C. / Edwards, A.M. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human SLK bound to a maleimide inhibitor
Authors: Sorrell, F.J. / Berger, B.T. / Salah, E. / Serafim, R.A.M. / Elkins, J.M.
History
DepositionOct 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4207
Polymers34,6901
Non-polymers7306
Water4,306239
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-10 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.871, 69.871, 164.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-405-

SO4

21A-405-

SO4

31A-503-

HOH

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Components

#1: Protein STE20-like serine/threonine-protein kinase / hSLK / CTCL tumor antigen se20-9 / STE20-related serine/threonine-protein kinase / STE20-related ...hSLK / CTCL tumor antigen se20-9 / STE20-related serine/threonine-protein kinase / STE20-related kinase / Serine/threonine-protein kinase 2


Mass: 34690.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLK, KIAA0204, STK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2G2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GUQ / 3-(1,3-benzothiazol-2-ylamino)-4-(2-methoxyphenyl)pyrrole-2,5-dione


Mass: 351.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20M Na2SO4; 0.1M BTProp pH 8.5; 20.0% PEG 3350; 10.0% EtGly

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.63→64.298 Å / Num. obs: 51803 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 26.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Net I/σ(I): 20
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 12.9 % / Num. unique obs: 3773 / CC1/2: 0.589 / Rpim(I) all: 0.756 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.61 Å64.3 Å
Translation5.61 Å64.3 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jfm

2jfm


Resolution: 1.63→64.298 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.74
RfactorNum. reflection% reflection
Rfree0.2075 2559 4.97 %
Rwork0.1864 --
obs0.1874 51469 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.72 Å2 / Biso mean: 41.5273 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 1.63→64.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 78 239 2536
Biso mean--43.76 43.3 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.63-1.6610.42661430.3946258396
1.661-1.69490.38531370.3696262598
1.6949-1.73180.35671640.3514263699
1.7318-1.77210.3291220.3119268599
1.7721-1.81640.27641310.2995266699
1.8164-1.86550.30461460.2661267399
1.8655-1.92040.26471320.2476268199
1.9204-1.98240.21371490.20962693100
1.9824-2.05330.20011380.1952715100
2.0533-2.13550.18751300.17642700100
2.1355-2.23270.19021430.17212711100
2.2327-2.35040.17381440.16742727100
2.3504-2.49770.23031480.16742714100
2.4977-2.69050.18791420.16172747100
2.6905-2.96130.18631280.17362760100
2.9613-3.38970.18981400.17662786100
3.3897-4.27060.18451480.15092818100
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)
12.2876-0.8651-0.26922.89350.48871.70130.0383-0.12750.26380.1773-0.07910.0044-0.3476-0.16980.03850.27820.01550.00380.2641-0.01430.227310.486290.858812.1866
21.3130.4548-0.9880.7895-0.44921.0575-0.02920.0645-0.07510.022-0.0331-0.16650.00070.10430.06470.17990.005-0.01170.2430.02340.288417.200170.88399.7941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 18:182)A18 - 182
2X-RAY DIFFRACTION2(chain A and resid 189:309)A189 - 309

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