PDB-8p4h: Crystal structure of human methionine adenosyltransferase 2A (MAT...

ID or keywords:

Entry

Database: PDB / ID: 8p4h

Title

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric compound IDEAYA cmpd A

Components

S-adenosylmethionine synthase isoform type-2

Keywords

TRANSFERASE / METHIONINE ADENOSYLTRANSFERASE / SAM / ALLOSTERIC INHIBITOR / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.71 Å

Authors

Thomsen, M. / Thieulin-Pardo, G. / Neumann, L.

Funding support

1items

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Discovery of novel methionine adenosyltransferase 2A (MAT2A) allosteric inhibitors by structure-based virtual screening.
Authors: Kalliokoski, T. / Kettunen, H. / Kumpulainen, E. / Kettunen, E. / Thieulin-Pardo, G. / Neumann, L. / Thomsen, M. / Paul, R. / Malyutina, A. / Georgiadou, M.

History

Deposition	May 21, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p4h.cif.gz	626.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8p4h.ent.gz	513.5 KB	Display	PDB format
PDBx/mmJSON format	8p4h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8p4h_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8p4h_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8p4h_validation.xml.gz	64.8 KB	Display
Data in CIF	8p4h_validation.cif.gz	94.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p4/8p4h ftp://data.pdbj.org/pub/pdb/validation_reports/p4/8p4h	HTTPS FTP

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Related structure data

Related structure data	8p1tC 8p1vC 8p1wC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: S-adenosylmethionine synthase isoform type-2

B: S-adenosylmethionine synthase isoform type-2

C: S-adenosylmethionine synthase isoform type-2

D: S-adenosylmethionine synthase isoform type-2

hetero molecules

186 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: S-adenosylmethionine synthase isoform type-2

B: S-adenosylmethionine synthase isoform type-2

hetero molecules

defined by author&software
93 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: S-adenosylmethionine synthase isoform type-2

D: S-adenosylmethionine synthase isoform type-2

hetero molecules

defined by author&software
92.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.898, 106.742, 114.996
Angle α, β, γ (deg.)	90.00, 93.18, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2
3	3
4	4
5	5
6	6

/ NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II Mass: 45719.680 Da / Num. of mol.: 4 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

#1: Protein

S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II

Mass: 45719.680 Da / Num. of mol.: 4
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, 1092 molecules

#2: Chemical	ChemComp-UM6 / 7-chloranyl-4-[(3R)-3-fluoranylpyrrolidin-1-yl]-1-phenyl-quinazolin-2-one Mass: 343.783 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₈H₁₅ClFN₃O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1075 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 45.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.10 M HEPES pH 7.0, 20 % (w/v) PEG 6000, 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.71→78.3 Å / Num. obs: 176313 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC_1/2: 0.998 / R_pim(I) all: 0.041 / R_rim(I) all: 0.086 / R_sym value: 0.076 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.71→1.74 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 12 / Num. unique obs: 8792 / CC_1/2: 0.75 / R_pim(I) all: 0.509 / R_rim(I) all: 1.073 / R_sym value: 0.94 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.71→78.3 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.967 / SU B: 4.915 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18388	8747	5 %	RANDOM
R_work	0.15278	-	-	-
obs	0.15433	167555	99.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.045 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.65 Å²	0 Å²	0.18 Å²
2-	-	0.68 Å²	0 Å²
3-	-	-	-1.35 Å²

Refinement step

Cycle: 1 / Resolution: 1.71→78.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11771	0	196	1075	13042

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	12280
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	11463
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.654	16655
X-RAY DIFFRACTION	r_angle_other_deg	1.44	1.589	26542
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.073	5	1546
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.084	22.075	617
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.85	15.036	2062
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.547	15	77
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	1583
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	13891
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2542
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.393	2.205	6139
X-RAY DIFFRACTION	r_mcbond_other	2.384	2.205	6139
X-RAY DIFFRACTION	r_mcangle_it	3.037	3.697	7691
X-RAY DIFFRACTION	r_mcangle_other	3.037	3.698	7692
X-RAY DIFFRACTION	r_scbond_it	3.948	2.693	6141
X-RAY DIFFRACTION	r_scbond_other	3.948	2.694	6142
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.221	4.329	8962
X-RAY DIFFRACTION	r_long_range_B_refined	6.971	21.849	13657
X-RAY DIFFRACTION	r_long_range_B_other	6.948	21.217	13438
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4454	0.04
1	2	B	4454	0.04
2	1	A	4577	0.04
2	2	C	4577	0.04
3	1	A	4560	0.04
3	2	D	4560	0.04
4	1	B	4498	0.04
4	2	C	4498	0.04
5	1	B	4504	0.03
5	2	D	4504	0.03
6	1	C	4537	0.04
6	2	D	4537	0.04

LS refinement shell

Resolution: 1.71→1.754 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	586	-
R_work	0.325	12399	-
obs	-	-	99.87 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.608	-0.2208	-2.7164	2.0117	1.6538	13.5308	-0.0828	0.5433	-0.2097	-0.4144	-0.0351	0.0105	0.4527	-0.579	0.118	0.1874	-0.0277	0.0023	0.186	-0.0259	0.1014	1.948	-8.344	-16.045
2	1.0985	0.6163	-0.0344	1.8941	-0.3249	0.9416	0.061	-0.0879	0.0477	0.13	-0.0805	0.0002	-0.0755	-0.0421	0.0196	0.0753	0.0107	-0.0058	0.159	-0.0188	0.0046	2.206	6.596	21.958
3	3.2885	-2.6823	2.7526	6.732	-4.1918	7.3058	-0.0794	-0.0533	0.4222	0.1739	-0.0815	0.0184	-0.4682	-0.1184	0.161	0.1578	-0.0015	-0.0078	0.1856	-0.0241	0.1568	16.646	26.466	13.677
4	1.3231	0.7207	-0.3027	1.2478	-0.055	1.1057	-0.0563	0.081	-0.0985	-0.063	0.0338	0.0745	0.1657	-0.1953	0.0224	0.0857	0.0067	-0.0198	0.1371	-0.0222	0.0322	-4.34	-5.535	0.209
5	0.9311	0.2603	0.0691	1.1542	-0.0569	2.1205	-0.0412	0.0869	0.1604	-0.1043	0.0023	0.0989	-0.2776	-0.1341	0.0388	0.1248	0.0235	-0.0402	0.1126	0.0048	0.0387	6.037	17.844	-3.177
6	3.1426	-1.2884	3.9585	3.6993	-3.4841	11.0961	-0.0946	0.2122	0.1783	-0.3186	-0.0731	-0.0498	0.0746	0.2529	0.1677	0.1042	-0.0212	0.0077	0.1179	-0.0096	0.0627	22.456	12.899	-7.063
7	1.2298	0.0201	0.3928	1.295	1.5074	3.3649	0.0934	-0.1128	-0.2248	0.2599	-0.0953	-0.0058	0.539	0.0588	0.0019	0.1768	0.0383	-0.033	0.1749	0.0328	0.0731	23.32	-5.721	20.582
8	5.11	3.9535	-0.766	5.7906	1.1357	9.965	-0.1206	-0.3749	-0.9026	0.0764	0.4482	-0.7808	1.8258	0.8385	-0.3275	0.4771	0.1439	-0.0071	0.3163	0.1222	0.5495	12.233	-24.784	5.101
9	1.023	0.4615	0.2551	1.0491	0.1378	1.6658	-0.0504	0.0475	0.0461	-0.057	0.0366	-0.1534	-0.23	0.4108	0.0139	0.0819	-0.0127	0.0007	0.2119	0.0061	0.0396	29.28	11.239	2.096
10	1.1664	0.3877	0.0908	1.2456	0.0531	2.377	-0.0027	0.0939	-0.2702	-0.0659	0.039	-0.1563	0.4124	0.2609	-0.0363	0.1618	0.0446	0.011	0.15	-0.0253	0.0676	19.093	-11.042	-6.429
11	1.4469	-0.0772	-1.9716	7.943	-8.6548	13.0191	-0.2649	-0.2781	-0.1165	0.692	-0.1385	-0.341	-0.5538	0.6536	0.4033	0.1566	0.0256	0.0157	0.3043	0.0098	0.0682	26.303	-2.575	69.766
12	2.1525	-0.387	-0.7188	1.1925	0.2469	2.376	-0.0233	0.0814	0.0848	-0.0242	-0.0104	0.102	-0.1765	-0.122	0.0336	0.0933	-0.015	-0.0287	0.1748	0.0037	0.0223	14.114	10.545	40.033
13	7.5966	1.9641	3.7616	9.2529	5.3853	4.1274	0.0013	0.0535	1.509	-0.0103	-0.3717	-0.3792	-0.1287	-0.2589	0.3704	0.6977	0.0774	-0.1183	0.4801	0.115	0.4061	-9.493	10.364	53.021
14	1.78	0.1071	-0.4033	0.5607	-0.2635	0.9855	0.0039	-0.1676	0.0581	0.0203	-0.0179	-0.0959	-0.0439	0.2889	0.0141	0.0682	-0.0015	-0.0225	0.261	-0.0218	0.0265	29.413	4.528	59.846
15	1.3835	0.1315	-0.2091	1.1144	-0.3028	3.0369	0.0034	-0.1469	0.2451	0.0532	0.008	0.1548	-0.3449	-0.1265	-0.0113	0.0925	0.0235	-0.0065	0.231	-0.0402	0.062	5.081	9.707	66.271
16	1.6351	-0.2872	-0.6151	2.2874	2.061	13.2975	-0.1228	-0.3354	0.0542	0.423	-0.0266	0.253	0.0612	-0.5098	0.1495	0.1314	0.0054	0.0303	0.2722	0.0054	0.0938	-3.933	-5.824	74.073
17	2.3653	-0.7111	1.6505	1.5044	-0.6412	2.9036	0.0651	0.288	-0.0693	-0.0848	-0.0769	-0.1603	0.2714	0.4357	0.0118	0.1317	0.0298	0.0061	0.2238	-0.0139	0.0294	10.968	-13.704	37.503
18	6.1558	0.2634	-1.7054	3.8952	-0.1602	12.2728	0.4523	0.3643	-1.0625	-0.4866	-0.3238	-0.5659	1.5665	1.6312	-0.1285	0.5718	0.187	0.1011	0.5851	-0.1745	0.5686	34.455	-18.837	52.237
19	1.8885	0.0603	0.2757	0.5141	0.1933	1.4442	0.0283	-0.1483	-0.0753	0.0537	-0.026	0.1032	0.156	-0.228	-0.0022	0.0912	-0.0091	0.0099	0.1834	0.0023	0.0257	-4.414	-11.679	58.055
20	1.6778	0.2022	0.2975	1.4478	0.1124	2.1681	0.0328	-0.0739	-0.2645	0.0531	0.023	-0.1387	0.3973	0.2563	-0.0559	0.1328	0.0637	-0.0168	0.2566	0.0282	0.058	19.914	-18.246	63.351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 26
2	X-RAY DIFFRACTION	2	A	27 - 113
3	X-RAY DIFFRACTION	3	A	114 - 133
4	X-RAY DIFFRACTION	4	A	134 - 274
5	X-RAY DIFFRACTION	5	A	275 - 395
6	X-RAY DIFFRACTION	6	B	15 - 26
7	X-RAY DIFFRACTION	7	B	27 - 113
8	X-RAY DIFFRACTION	8	B	114 - 133
9	X-RAY DIFFRACTION	9	B	134 - 274
10	X-RAY DIFFRACTION	10	B	275 - 395
11	X-RAY DIFFRACTION	11	C	14 - 26
12	X-RAY DIFFRACTION	12	C	27 - 113
13	X-RAY DIFFRACTION	13	C	114 - 133
14	X-RAY DIFFRACTION	14	C	134 - 274
15	X-RAY DIFFRACTION	15	C	275 - 395
16	X-RAY DIFFRACTION	16	D	9 - 26
17	X-RAY DIFFRACTION	17	D	27 - 113
18	X-RAY DIFFRACTION	18	D	114 - 133
19	X-RAY DIFFRACTION	19	D	134 - 274
20	X-RAY DIFFRACTION	20	D	275 - 395

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 1092 molecules

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