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- PDB-7kce: Crystal structure of human methionine adenosyltransferase 2A (MAT... -

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Basic information

Entry
Database: PDB / ID: 7kce
TitleCrystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 2
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE/Inhibitor / METHIONINE ADENOSYLTRANSFERASE / S-adenosylmethionine synthase isoform type-2 / SAM / Allosteric Inhibitor / TRANSFERASE / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
Chem-J41 / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPadyana, A. / Jin, L.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of AG-270, a First-in-Class Oral MAT2A Inhibitor for the Treatment of Tumors with Homozygous MTAP Deletion.
Authors: Konteatis, Z. / Travins, J. / Gross, S. / Marjon, K. / Barnett, A. / Mandley, E. / Nicolay, B. / Nagaraja, R. / Chen, Y. / Sun, Y. / Liu, Z. / Yu, J. / Ye, Z. / Jiang, F. / Wei, W. / Fang, C. ...Authors: Konteatis, Z. / Travins, J. / Gross, S. / Marjon, K. / Barnett, A. / Mandley, E. / Nicolay, B. / Nagaraja, R. / Chen, Y. / Sun, Y. / Liu, Z. / Yu, J. / Ye, Z. / Jiang, F. / Wei, W. / Fang, C. / Gao, Y. / Kalev, P. / Hyer, M.L. / DeLaBarre, B. / Jin, L. / Padyana, A.K. / Dang, L. / Murtie, J. / Biller, S.A. / Sui, Z. / Marks, K.M.
History
DepositionOct 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5434
Polymers43,8081
Non-polymers7353
Water9,818545
1
A: S-adenosylmethionine synthase isoform type-2
hetero molecules

A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0868
Polymers87,6152
Non-polymers1,4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6890 Å2
ΔGint-51 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.970, 94.240, 116.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-660-

HOH

31A-874-

HOH

41A-907-

HOH

51A-1010-

HOH

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Components

#1: Protein S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43807.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical ChemComp-J41 / 5-methyl-2,3-diphenylpyrazolo[1,5-a]pyrimidin-7(4H)-one


Mass: 301.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M Lithium Chloride, 0.1M Tris PH 7.8, 20% PEG 6000, 10% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.14→29.37 Å / Num. obs: 131343 / % possible obs: 97.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.44 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.1
Reflection shellResolution: 1.14→1.17 Å / Redundancy: 3 % / Rmerge(I) obs: 0.483 / Num. unique obs: 8683 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P02

2p02


Resolution: 1.14→29.37 Å / SU ML: 0.071 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1587 6614 5.04 %
Rwork0.1436 124714 -
obs0.1444 131328 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.35 Å2
Refinement stepCycle: LAST / Resolution: 1.14→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 51 545 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063306
X-RAY DIFFRACTIONf_angle_d1.19834516
X-RAY DIFFRACTIONf_chiral_restr0.0965494
X-RAY DIFFRACTIONf_plane_restr0.0098601
X-RAY DIFFRACTIONf_dihedral_angle_d17.22041296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.22792030.22453542X-RAY DIFFRACTION83.93
1.15-1.170.22751780.22623817X-RAY DIFFRACTION89.59
1.17-1.180.22712040.21664042X-RAY DIFFRACTION94.71
1.18-1.20.21772190.21144183X-RAY DIFFRACTION97.78
1.2-1.210.21852340.22314185X-RAY DIFFRACTION98.55
1.21-1.230.20442190.21724217X-RAY DIFFRACTION98.64
1.23-1.250.24332170.20734174X-RAY DIFFRACTION98.83
1.25-1.270.22512350.20134193X-RAY DIFFRACTION98.71
1.27-1.290.20592070.19654215X-RAY DIFFRACTION98.71
1.29-1.310.20522580.19334207X-RAY DIFFRACTION99.13
1.31-1.330.20072200.18844205X-RAY DIFFRACTION98.9
1.33-1.350.18472020.17674233X-RAY DIFFRACTION99.28
1.35-1.380.19152220.17464217X-RAY DIFFRACTION98.97
1.38-1.410.18982240.16674231X-RAY DIFFRACTION99.31
1.41-1.440.18622000.17044290X-RAY DIFFRACTION99.36
1.44-1.470.16162140.15084262X-RAY DIFFRACTION99.44
1.47-1.510.15982340.15784196X-RAY DIFFRACTION98.66
1.51-1.550.1652110.14524240X-RAY DIFFRACTION98.76
1.55-1.60.15312090.13494239X-RAY DIFFRACTION99.35
1.6-1.650.15492430.13184248X-RAY DIFFRACTION99.01
1.65-1.710.15392280.13264240X-RAY DIFFRACTION99.13
1.71-1.770.14832090.13394225X-RAY DIFFRACTION98.86
1.77-1.850.14172210.13064233X-RAY DIFFRACTION98.21
1.85-1.950.14872190.13974078X-RAY DIFFRACTION94.79
1.95-2.070.1382370.11974106X-RAY DIFFRACTION95.58
2.07-2.230.13022480.12044147X-RAY DIFFRACTION96.53
2.23-2.460.14822410.12124102X-RAY DIFFRACTION95.56
2.46-2.810.1362150.12074280X-RAY DIFFRACTION97.85
2.82-3.550.14032430.11944277X-RAY DIFFRACTION97.84
3.55-29.370.14392000.13153890X-RAY DIFFRACTION85.39
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)
10.422477658472-0.1495769312650.1270815061570.489938050403-0.1710058817810.462353805155-0.01360470431680.006931364289530.01417369497180.02359537754610.0103542088403-0.0510515161804-0.004507343957330.06804777126430.005658693356340.0636378106155-0.0004468472689020.0003613429044280.071737555758-0.007849291734870.0687354675149.263889566595.18805247985-15.7804477455
20.810854301321-0.292586169331-0.02224069917251.95265420750.0831631151061.25929179752-0.0357921355623-0.02234582234630.1204028855230.09017207397380.0280265838117-0.077493518323-0.08278883382180.1715790633970.01507027696420.0911686903329-0.0114001185109-0.007722147768320.101574348079-0.00151650790890.08289326263597.2695126757516.0215273397-5.5661642979
30.161308823445-0.1621761105750.005450725474240.604444632913-0.08800424177340.304157236416-0.004735585288280.01330209026440.0231229577887-0.02790199148390.000986389630414-0.06751643720580.01009549476340.04737287701870.0062116735690.0564428401279-0.009887092082360.001262258552010.08618913145920.0008208300190960.086683505633712.22919900312.08491676236-24.1853674957
40.723387602152-0.07473293576630.1421113668191.016823215660.2099872295011.003648620960.001668145987130.08495197080710.0954348272252-0.1153774643250.02031429257140.00950779742423-0.1104666344790.0227316010111-0.01700804897290.0747527077444-0.00391841510112-0.0005491928085140.07699336798540.02306762086590.0943196406469-3.862894017423.8752579518-30.8534113502
50.380541648568-0.212970585997-0.04229860154010.5585925189610.08640343348810.2419081394770.005868748854770.05619448401640.00224733091506-0.0988905363105-0.00157159615088-0.0195523580567-0.01740793276110.0145851810324-0.005239057868750.0753292988715-0.008656830699140.00274062562680.07358050253470.003288163195980.06451340910968.318770010971.81577604223-31.6602679818
60.794447690723-0.3939317312870.01027354558761.08628087153-0.7970252853261.232850916580.03124999799420.208435100276-0.0532156353525-0.389736475349-0.0683302836075-0.1736594125340.2649446379830.126359212790.01343254574020.171265326680.01231375747140.04042540102670.111656612571-0.002968845577570.11120414660221.461732065-5.27463196973-38.7043813502
71.08434257377-0.02577030110430.01091270834430.750948410431-0.4549163848351.01109953453-0.03206665962670.06868298739570.114936178775-0.08398510635990.0177176082964-0.163458633558-0.04899068588070.115341407628-0.002058760099450.0929254257112-0.0190734257270.01327836650980.0916629596571-0.0008559785516590.11113698885119.00705243167.70986379434-30.0159132209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 169 )
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 244 )
5X-RAY DIFFRACTION5chain 'A' and (resid 245 through 341 )
6X-RAY DIFFRACTION6chain 'A' and (resid 342 through 364 )
7X-RAY DIFFRACTION7chain 'A' and (resid 365 through 395 )

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