SMTL ID : 7rxv.1

Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine, Malonate (MLA) and MgF3

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: 20 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, G.155, D.156, I.344 Ligands: ALA.2, MLA.3 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.201, A:R.271 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.10: 20 residues within 4Å: Chain A: S.136, D.138, I.139, 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.11, MLA.12 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Water bridges: A:I.139, A:I.139, B:D.201, B:S.269, B:G.276 Hydrogen bonds: B:D.201, B:R.271 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, MLA.3 10 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.92, B:E.92, B:Q.135, A.2 Water bridges: B:K.311, B:K.311, B:K.311, B:K.311, A:A.281 Salt bridges: B:K.311 ALA.11: 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.10, MLA.12 11 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.280, A:E.92, A:E.92, A:Q.135, A.11 Water bridges: B:A.281, A:K.311, A:K.311, A:K.311, A:K.311 Salt bridges: A:K.311

2 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 14 residues within 4Å: Chain A: H.51, D.53, K.203, D.280, R.286, K.287 Chain B: D.156, K.307, D.313 Ligands: MTA.1, ALA.2, MGF.4, MG.6, K.7 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.51, A:K.203, A:R.286, A:K.287, B:K.307 Water bridges: B:D.156 MLA.12: 14 residues within 4Å: Chain A: D.156, K.307, D.313 Chain B: H.51, D.53, K.203, D.280, R.286, K.287 Ligands: MTA.10, ALA.11, MGF.13, MG.15, K.16 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:D.156 Salt bridges: A:K.307, B:H.51, B:K.203, B:R.286, B:K.287

2 x MGF: TRIFLUOROMAGNESATE(Non-covalent)

MGF.4: 9 residues within 4Å: Chain A: D.53, R.286, K.287 Chain B: G.302, A.303, K.307, D.313 Ligands: MLA.3, MG.6 No protein-ligand interaction detected (PLIP) MGF.13: 9 residues within 4Å: Chain A: G.302, A.303, K.307, D.313 Chain B: D.53, R.286, K.287 Ligands: MLA.12, MG.15 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: F.40, F.42, Q.212, V.217, W.296, R.335, Y.357 Chain B: L.337, F.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.212, A:R.335, A:R.335 GOL.14: 9 residues within 4Å: Chain A: L.337, F.355 Chain B: F.40, F.42, Q.212, V.217, W.296, R.335, Y.357 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.212, B:R.335, B:R.335

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: H.51, D.53, R.286, K.287 Ligands: MLA.3, MGF.4, K.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, H2O.2, H2O.2 MG.15: 7 residues within 4Å: Chain B: H.51, D.53, R.286, K.287 Ligands: MLA.12, MGF.13, K.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.53, H2O.16, H2O.17

2 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: D.280, A.281 Chain B: E.79 Ligands: MLA.3, MG.6 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.16: 5 residues within 4Å: Chain A: E.79 Chain B: D.280, A.281 Ligands: MLA.12, MG.15 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.4

4 x NA: SODIUM ION(Non-functional Binders)

NA.8: 7 residues within 4Å: Chain A: A.154, Y.342, A.343, V.346, H.348, P.349, L.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.343, A:V.346 NA.9: 5 residues within 4Å: Chain A: R.221, H.223, D.261, T.262, I.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.221, A:R.221, A:D.261 NA.17: 7 residues within 4Å: Chain B: A.154, Y.342, A.343, V.346, H.348, P.349, L.350 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.343, B:A.343 NA.18: 5 residues within 4Å: Chain B: R.221, H.223, D.261, T.262, I.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.221, B:R.221, B:H.223

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

2021-11-03

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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