SMTL ID : 7rxw.1

Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine and inhibitor imido-diphosphate (PNP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

homo-dimer

Ligands

2 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 21 residues within 4Å: Chain A: H.51, P.52, D.201, K.203, S.228, S.269, R.271, F.272, I.274, G.275, G.279, D.280 Chain B: S.136, D.138, I.139, Q.141, G.155, D.156, I.344 Ligands: ALA.2, 2PN.3 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.201, B:D.138 Water bridges: A:D.201, A:S.269, A:G.276, B:I.139, B:I.139 pi-Stacking: A:F.272, A:F.272 MTA.8: 21 residues within 4Å: Chain A: S.136, D.138, I.139, Q.141, G.155, D.156, I.344 Chain B: H.51, P.52, D.201, K.203, S.228, S.269, R.271, F.272, I.274, G.275, G.279, D.280 Ligands: ALA.9, 2PN.10 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.201, A:D.138 Water bridges: B:D.201, B:S.269, B:G.276, A:I.139, A:I.139 pi-Stacking: B:F.272, B:F.272

2 x ALA: ALANINE(Non-covalent)

ALA.2: 10 residues within 4Å: Chain A: G.279, D.280 Chain B: A.77, E.92, Q.135, I.139, G.155, K.311 Ligands: MTA.1, 2PN.3 10 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: A.2, B:E.92, B:E.92, B:Q.135 Water bridges: B:K.311, B:K.311, B:K.311, B:K.311, A:A.281 Salt bridges: B:K.311 ALA.9: 10 residues within 4Å: Chain A: A.77, E.92, Q.135, I.139, G.155, K.311 Chain B: G.279, D.280 Ligands: MTA.8, 2PN.10 10 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.92, A:E.92, A:Q.135, A.9 Water bridges: A:K.311, A:K.311, A:K.311, A:K.311, B:A.281 Salt bridges: A:K.311

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.3: 15 residues within 4Å: Chain A: H.51, D.53, K.203, D.280, R.286, K.287 Chain B: E.79, D.156, K.307, D.313 Ligands: MTA.1, ALA.2, MG.5, MG.6, K.7 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:H.51, A:K.203, A:R.286, A:K.287, B:D.156, B:D.156, B:K.307 Water bridges: A:D.53, A:D.53, A:D.53, A:D.280, A:A.281, A:R.286, A:R.286, B:D.156, B:D.313, B:D.313, B:D.313 2PN.10: 15 residues within 4Å: Chain A: E.79, D.156, K.307, D.313 Chain B: H.51, D.53, K.203, D.280, R.286, K.287 Ligands: MTA.8, ALA.9, MG.12, MG.13, K.14 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:H.51, B:K.203, B:R.286, B:K.287, A:D.156, A:D.156, A:K.307 Water bridges: B:D.53, B:D.53, B:D.53, B:D.280, B:A.281, B:R.286, B:R.286, A:D.156, A:D.313, A:D.313, A:D.313

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: R.241, Y.264, H.265, L.266, Q.267, P.268 Chain B: V.346 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.265, A:L.266 EDO.11: 7 residues within 4Å: Chain A: V.346 Chain B: R.241, Y.264, H.265, L.266, Q.267, P.268 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.265, B:L.266

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: H.51, D.53, R.286, K.287 Ligands: 2PN.3, K.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.53, H2O.1, H2O.1, H2O.3 MG.6: 5 residues within 4Å: Chain A: K.287 Chain B: G.302, K.307, D.313 Ligands: 2PN.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.313, H2O.1, H2O.2, H2O.17, H2O.23 MG.12: 6 residues within 4Å: Chain B: H.51, D.53, R.286, K.287 Ligands: 2PN.10, K.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.53, H2O.17, H2O.17, H2O.18 MG.13: 5 residues within 4Å: Chain A: G.302, K.307, D.313 Chain B: K.287 Ligands: 2PN.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.313, H2O.1, H2O.8, H2O.17, H2O.18

2 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: D.280, A.281 Chain B: E.79 Ligands: 2PN.3, MG.5 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.280, A:A.281, B:E.79, H2O.18 K.14: 5 residues within 4Å: Chain A: E.79 Chain B: D.280, A.281 Ligands: 2PN.10, MG.12 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.280, B:A.281, A:E.79, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A. et al., Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 angstrom Resolution. J.Am.Chem.Soc. (2021)

Release Date

2021-11-10

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-adenosylmethionine synthase isoform type-2

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