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

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Basic information

Entry
Database: PDB / ID: 7kda
TitleCrystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 34
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE/Inhibitor / METHIONINE ADENOSYLTRANSFERASE / 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 / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / 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
S-ADENOSYLMETHIONINE / Chem-WBM / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 8, 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)44,8246
Polymers43,8081
Non-polymers1,0175
Water8,629479
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)89,64812
Polymers87,6152
Non-polymers2,03310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7870 Å2
ΔGint-44 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.124, 94.028, 116.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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-655-

HOH

21A-749-

HOH

31A-943-

HOH

41A-1058-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 484 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H22N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-WBM / 2,3-diphenyl-5-[(1H-pyrazol-3-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one


Mass: 368.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N6O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2 M Lithium Chloride, 0.1 M 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: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.24→30.27 Å / Num. obs: 105080 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 9.14 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.7
Reflection shellResolution: 1.24→1.29 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 10329 / % possible all: 98.2

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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
Resolution: 1.24→30.27 Å / SU ML: 0.072 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.789
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.139 5134 4.89 %
Rwork0.127 --
obs0.127 105066 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.74 Å2
Refinement stepCycle: LAST / Resolution: 1.24→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 70 479 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013221
X-RAY DIFFRACTIONf_angle_d1.1674391
X-RAY DIFFRACTIONf_dihedral_angle_d19.6891225
X-RAY DIFFRACTIONf_chiral_restr0.091483
X-RAY DIFFRACTIONf_plane_restr0.009567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.18511470.17113265X-RAY DIFFRACTION98
1.26-1.270.17361960.1623299X-RAY DIFFRACTION100
1.27-1.290.16341910.15613297X-RAY DIFFRACTION100
1.29-1.30.1611670.14873307X-RAY DIFFRACTION100
1.3-1.320.17551630.15163315X-RAY DIFFRACTION100
1.32-1.340.13611750.14553325X-RAY DIFFRACTION100
1.34-1.360.14011600.14763294X-RAY DIFFRACTION100
1.36-1.380.15841630.14133359X-RAY DIFFRACTION100
1.38-1.40.16261680.13823335X-RAY DIFFRACTION100
1.4-1.420.17331570.13953356X-RAY DIFFRACTION100
1.42-1.450.14281520.13663328X-RAY DIFFRACTION100
1.45-1.470.14991820.1293312X-RAY DIFFRACTION100
1.47-1.50.14411540.12693335X-RAY DIFFRACTION100
1.5-1.530.12431640.12473323X-RAY DIFFRACTION100
1.53-1.560.13741380.12023366X-RAY DIFFRACTION100
1.56-1.60.13191680.12143317X-RAY DIFFRACTION100
1.6-1.640.14621790.1193328X-RAY DIFFRACTION100
1.64-1.690.1241680.11573357X-RAY DIFFRACTION100
1.69-1.740.12881700.11533345X-RAY DIFFRACTION100
1.74-1.790.13642060.11863319X-RAY DIFFRACTION100
1.79-1.860.12651770.11933307X-RAY DIFFRACTION100
1.86-1.930.13551780.11943364X-RAY DIFFRACTION100
1.93-2.020.12171970.11683328X-RAY DIFFRACTION100
2.02-2.120.13091780.11533345X-RAY DIFFRACTION100
2.12-2.260.12581720.11413358X-RAY DIFFRACTION100
2.26-2.430.13481740.1153393X-RAY DIFFRACTION100
2.43-2.680.1281970.11473354X-RAY DIFFRACTION100
2.68-3.060.13631570.12013417X-RAY DIFFRACTION100
3.06-3.860.13141540.12143396X-RAY DIFFRACTION98
3.86-30.270.15131820.15223188X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0616-0.370.63290.536-0.31870.6794-0.00880.06650.0135-0.02820.0105-0.0074-0.02490.07290.03840.0546-0.00330.00190.0589-0.00070.05686.0459.1947-22.5828
20.3678-0.5244-0.49351.22390.39230.7855-0.0372-0.0215-0.04540.04410.0135-0.0073-0.01230.06090.02870.09080.003-0.00610.0953-0.00340.08212.38750.5355-9.1524
30.1357-0.1029-0.01570.43780.01040.195-0.0237-0.0253-0.00070.0530.027-0.0260.01920.0392-0.02570.0679-0.0019-0.00320.09080.00090.080711.72091.5009-13.2797
40.1293-0.2822-0.03572.20421.87232.91370.0287-0.01510.0369-0.05710.0237-0.1013-0.08040.0727-0.07090.0732-0.01130.00080.07650.01490.08886.328418.4827-31.1656
50.7604-0.16810.08081.16210.25681.11340.01520.03550.085-0.04470.00530.0037-0.06090.001-0.0140.0408-0.00090.00180.05010.01650.0667-3.697722.9483-28.1417
63.07731.2671-0.72321.08350.19642.6839-0.05490.18960.2366-0.17790.09560.0727-0.17670.04290.02130.10670.0069-0.00230.05780.03130.1018-3.781327.0157-35.2397
70.2946-0.1248-0.00780.30320.03430.17240.00610.0390.0011-0.0577-0.0045-0.0098-0.00710.0157-0.00620.0797-0.00550.00480.07920.00520.06848.21271.7861-31.4819
81.5933-0.74470.46470.6087-0.90073.37670.09370.2079-0.022-0.273-0.0888-0.10720.29510.1043-0.04510.14490.01320.03110.08860.00340.084521.0905-5.409-38.8307
91.1798-0.0140.14870.8915-0.25841.3604-0.03770.10240.1093-0.08350.0187-0.1491-0.06090.0938-0.04930.0779-0.01860.01170.07940.00270.095318.95347.7099-29.8428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 15 THROUGH 48 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 49 THROUGH 78 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 79 THROUGH 143 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 144 THROUGH 169 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 170 THROUGH 224 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 225 THROUGH 244 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 245 THROUGH 341 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 342 THROUGH 364 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 365 THROUGH 395 )

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