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- PDB-36wl: Mevalonate kinase from Saccharomyces cerevisiae with geranyl pyro... -

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Basic information

Entry
Database: PDB / ID: 36wl
TitleMevalonate kinase from Saccharomyces cerevisiae with geranyl pyrophosphate (GPP) bound
ComponentsMevalonate kinase
KeywordsTRANSFERASE / metabolic enzyme / mevalonate pathway
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / Lanosterol biosynthesis / ergosterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / farnesyl diphosphate biosynthetic process, mevalonate pathway / magnesium ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
beta-D-glucopyranose / GERANYL DIPHOSPHATE / D(-)-TARTARIC ACID / Mevalonate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsD'Emilia, R.L.S. / Ragwan, E.R. / Chang, V. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural basis of mevalonate pathway regulation by feedback inhibition of mevalonate kinase.
Authors: D'Emilia, R.L.S. / McCaskey, K.A. / Ragwan, E.R. / Kim, J.H. / Chang, V. / Tang, M.M. / Kung, Y.
History
DepositionJul 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1645
Polymers51,4951
Non-polymers6694
Water2,504139
1
A: Mevalonate kinase
hetero molecules

A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,32810
Polymers102,9912
Non-polymers1,3388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5810 Å2
ΔGint-39 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 83.450, 262.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Mevalonate kinase / MK / MvK / Ergosterol biosynthesis protein 12 / Regulation of autonomous replication protein 1


Mass: 51495.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERG12, RAR1, YMR208W, YM8261.02 / Production host: Escherichia coli (E. coli) / References: UniProt: P07277, mevalonate kinase
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 142 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 900-1100 mM sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→83.59 Å / Num. obs: 58995 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.24 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.9 % / Num. unique obs: 4515 / CC1/2: 0.849 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→79.54 Å / SU ML: 0.1748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 2944 5 %
Rwork0.1779 55915 -
obs0.1789 58859 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.56 Å2
Refinement stepCycle: LAST / Resolution: 2.05→79.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 42 139 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673574
X-RAY DIFFRACTIONf_angle_d0.86134853
X-RAY DIFFRACTIONf_chiral_restr0.0503568
X-RAY DIFFRACTIONf_plane_restr0.0056623
X-RAY DIFFRACTIONf_dihedral_angle_d14.01251310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.25911300.24192486X-RAY DIFFRACTION94.58
2.09-2.120.30761360.23372604X-RAY DIFFRACTION99.6
2.12-2.160.24841380.22512624X-RAY DIFFRACTION99.86
2.16-2.20.2381380.20932618X-RAY DIFFRACTION99.71
2.2-2.250.2241380.19762625X-RAY DIFFRACTION99.82
2.25-2.30.22981390.19192605X-RAY DIFFRACTION99.71
2.3-2.350.21631380.19432618X-RAY DIFFRACTION99.75
2.35-2.410.25061370.19712633X-RAY DIFFRACTION99.96
2.41-2.470.23011400.19632644X-RAY DIFFRACTION99.86
2.47-2.550.22531400.19572642X-RAY DIFFRACTION99.93
2.55-2.630.20461390.18682655X-RAY DIFFRACTION99.89
2.63-2.720.18261380.18782631X-RAY DIFFRACTION99.89
2.72-2.830.24371410.18912670X-RAY DIFFRACTION99.89
2.83-2.960.22381410.1842673X-RAY DIFFRACTION99.96
2.96-3.120.19391390.18422652X-RAY DIFFRACTION100
3.12-3.310.19741420.18782683X-RAY DIFFRACTION99.82
3.31-3.570.16571420.17452697X-RAY DIFFRACTION99.89
3.57-3.930.17631420.15522708X-RAY DIFFRACTION99.96
3.93-4.50.16141440.14992730X-RAY DIFFRACTION100
4.5-5.660.16261470.15622788X-RAY DIFFRACTION99.97
5.67-79.540.2111550.17612929X-RAY DIFFRACTION99.13
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)
11.327427626960.1992327262871.101482714360.4125668178450.3659060558181.39754331311-0.003772432753720.221144350271-0.114901844648-0.04703872481720.108596330378-0.0712370900426-0.02490594061350.1420642943230.009213034625790.175076916244-0.0136021288247-0.0008509948631040.335190837836-0.05838419224340.250220687727-3.15953347379-24.147084606331.0969460798
20.006666331254720.0322158654654-0.002226984078630.1482255396470.04252535595520.00497745005818-0.1393599005480.236596877551-0.224094628742-0.01023802633720.144181301674-0.2953713977240.3568813932870.1068123888584.87928610546E-70.3698017006230.0521913563262-0.0491395114240.353955098465-0.05501997381210.40926539693710.5990342107-31.011587164348.585070335
31.25786177021-0.09734904843850.4779303631110.7121471381240.3381201780541.403683184090.0628880942101-0.023020182086-0.06472003963250.0852809190677-0.03929408567150.06663006951490.0594732481167-0.197928416893-0.0006803879586980.2061260899650.0389879983172-0.009466222819420.252129802675-0.03390097712850.2258787434160.956034372911-16.1062609660.7634548942
40.2449701969060.08839353161260.2305256468010.158026125960.08594229408940.2159659002070.0256723220538-0.516047661272-0.0009648123734820.10514515198-0.08128214978180.0130597860675-0.013134160449-0.2674722838561.74988776861E-70.244406856262-0.01425921470550.001687991211880.509778016545-0.04693779239840.345713111281-20.8653185445-23.080244590840.0087918492
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -8 through 208 )-8 - 2081 - 217
22chain 'A' and (resid 209 through 231 )209 - 231218 - 240
33chain 'A' and (resid 232 through 391 )232 - 391241 - 400
44chain 'A' and (resid 392 through 443 )392 - 443401 - 452

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