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- PDB-8vf6: Crystal structure of Serine/threonine-protein kinase 33 (STK33) K... -

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Basic information

Entry
Database: PDB / ID: 8vf6
TitleCrystal structure of Serine/threonine-protein kinase 33 (STK33) Kinase Domain in complex with inhibitor CDD-2211
ComponentsSerine/threonine-protein kinase 33
KeywordsCYTOSOLIC PROTEIN / Kinase / STK33
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / calcium/calmodulin-dependent protein kinase activity / cellular response to oxidative stress / protein autophosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / ATP binding ...mitotic DNA damage checkpoint signaling / calcium/calmodulin-dependent protein kinase activity / cellular response to oxidative stress / protein autophosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase 33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTa, H.M. / Kim, C. / Ku, K.A. / Matzuk, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationNV- 001902 United States
CitationJournal: Science / Year: 2024
Title: Reversible male contraception by targeted inhibition of serine/threonine kinase 33.
Authors: Ku, A.F. / Sharma, K.L. / Ta, H.M. / Sutton, C.M. / Bohren, K.M. / Wang, Y. / Chamakuri, S. / Chen, R. / Hakenjos, J.M. / Jimmidi, R. / Kent, K. / Li, F. / Li, J.Y. / Ma, L. / Madasu, C. / ...Authors: Ku, A.F. / Sharma, K.L. / Ta, H.M. / Sutton, C.M. / Bohren, K.M. / Wang, Y. / Chamakuri, S. / Chen, R. / Hakenjos, J.M. / Jimmidi, R. / Kent, K. / Li, F. / Li, J.Y. / Ma, L. / Madasu, C. / Palaniappan, M. / Palmer, S.S. / Qin, X. / Robers, M.B. / Sankaran, B. / Tan, Z. / Vasquez, Y.M. / Wang, J. / Wilkinson, J. / Yu, Z. / Ye, Q. / Young, D.W. / Teng, M. / Kim, C. / Matzuk, M.M.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 33
B: Serine/threonine-protein kinase 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9384
Polymers65,0692
Non-polymers8692
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-23 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.210, 87.920, 98.150
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 Serine/threonine-protein kinase 33


Mass: 32534.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK33 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYT3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1AAY / {3-[([1,1'-biphenyl]-2-yl)ethynyl]-1H-indazol-5-yl}[(3R)-3-(dimethylamino)pyrrolidin-1-yl]methanone


Mass: 434.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium nitrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→43.96 Å / Num. obs: 20575 / % possible obs: 96.77 % / Redundancy: 2 % / CC1/2: 0.994 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1037 / CC1/2: 0.605 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5049: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.96 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 1038 5.04 %
Rwork0.2212 --
obs0.2229 20575 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4305 0 33 42 4380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034423
X-RAY DIFFRACTIONf_angle_d0.6655984
X-RAY DIFFRACTIONf_dihedral_angle_d18.3581610
X-RAY DIFFRACTIONf_chiral_restr0.048682
X-RAY DIFFRACTIONf_plane_restr0.004750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.38671420.35022731X-RAY DIFFRACTION100
2.84-3.020.31771470.30222752X-RAY DIFFRACTION100
3.02-3.250.32361480.30172760X-RAY DIFFRACTION100
3.25-3.580.30261430.25472757X-RAY DIFFRACTION100
3.58-4.10.24621530.2142777X-RAY DIFFRACTION100
4.1-5.160.20261450.17642823X-RAY DIFFRACTION100
5.16-43.960.23431600.19522937X-RAY DIFFRACTION100
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)
11.2633-0.78250.21531.62871.27091.7802-0.10120.1186-0.1076-0.13210.0034-0.17290.1598-0.09330.00010.4384-0.0409-0.0040.4929-0.00710.426-13.468516.9518-39.6311
20.9071-0.1387-0.00761.34351.49542.5532-0.12950.07440.1796-0.26840.09910.2803-0.1842-0.1334-0.00020.3611-0-0.01690.4320.06710.5192-16.257432.7808-30.6189
30.1151-0.27650.4661.2157-0.97741.653-0.07-0.12970.22610.32790.1285-0.1565-0.21360.03970.00010.46970.0075-0.01690.4801-0.09990.571-11.972235.9174-12.2565
42.1563-0.04380.04223.16460.68011.12740.1130.3905-0.12390.0686-0.10740.35230.0819-0.053-0.00010.48560.00580.04820.52750.01550.4898-7.2258-12.1619-4.1143
51.1733-0.28020.331.75451.18431.8518-0.1091-0.29010.05110.3107-0.0443-0.29440.1993-0.0262-0.00420.37390.0287-0.04630.4036-0.03890.2856-3.7885-0.07369.3439
6-0.00230.0508-0.05020.7365-0.79290.7772-0.20960.1283-0.0180.4012-0.2295-0.4338-0.2092-0.1109-0.01080.4785-0.0409-0.10280.41780.07380.5278-4.411918.9998-7.6391
70.8904-0.7148-0.25091.5465-0.08121.5508-0.2099-0.39750.52890.0572-0.05940.0459-0.8098-0.4773-0.00180.77530.0979-0.12150.7125-0.21640.5787-8.919418.142213.8277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 169 )
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 262 )
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 382 )
4X-RAY DIFFRACTION4chain 'B' and (resid 99 through 169 )
5X-RAY DIFFRACTION5chain 'B' and (resid 170 through 262 )
6X-RAY DIFFRACTION6chain 'B' and (resid 263 through 302 )
7X-RAY DIFFRACTION7chain 'B' and (resid 303 through 383 )

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