SMTL ID : 7rxx.1

Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine and two sulfate in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x ALA: ALANINE(Non-covalent)

ALA.1: 9 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.2 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.92, B:E.92, B:Q.135, A:D.280, A.1 Water bridges: B:K.311, B:K.311, B:K.311, B:K.311, A:A.281 Salt bridges: B:K.311 ALA.14: 9 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.15 11 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.92, A:E.92, A:Q.135, B:D.280, A.14 Water bridges: A:K.311, A:K.311, A:K.311, A:K.311, B:A.281 Salt bridges: A:K.311

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

MTA.2: 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.1, SO4.5 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.138, A:D.201 Water bridges: B:I.139, B:I.139, A:D.201, A:S.269, A:G.276 pi-Stacking: A:F.272, A:F.272 MTA.15: 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.14, SO4.18 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 P3G: 3,6,9,12,15-PENTAOXAHEPTADECANE(Non-covalent)

P3G.3: 19 residues within 4Å: Chain A: F.40, F.42, Q.212, G.215, V.217, W.296, R.335, L.337, F.355, Y.357 Chain B: F.42, W.296, R.335, L.337, F.355, Y.357 Ligands: NA.11, P3G.16, NA.24 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.335, A:R.335, A:R.335 Water bridges: B:G.297, B:Y.357, A:Y.357 Hydrophobic interactions: A:F.355 P3G.16: 19 residues within 4Å: Chain A: F.42, W.296, R.335, L.337, F.355, Y.357 Chain B: F.40, F.42, Q.212, G.215, V.217, W.296, R.335, L.337, F.355, Y.357 Ligands: P3G.3, NA.11, NA.24 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.355 Hydrogen bonds: B:R.335, B:R.335, A:R.335 Water bridges: B:Y.357, A:G.297, A:Y.357

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

EDO.4: 6 residues within 4Å: Chain A: D.73, K.75, T.94, A.140, H.144 Ligands: NA.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.75 Water bridges: A:T.94, A:H.144 EDO.17: 6 residues within 4Å: Chain B: D.73, K.75, T.94, A.140, H.144 Ligands: NA.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.75 Water bridges: B:T.94, B:H.144

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 10 residues within 4Å: Chain A: H.51, D.53, K.203, D.280, K.287 Chain B: D.156 Ligands: MTA.2, SO4.6, MG.7, MG.8 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.156, B:D.156 Water bridges: B:K.307, B:K.307, B:K.307, A:K.203, A:K.287 Salt bridges: A:H.51, A:K.203, A:K.287 SO4.6: 11 residues within 4Å: Chain A: D.53, R.286, K.287 Chain B: G.301, G.302, A.303, K.307, D.313 Ligands: SO4.5, MG.7, MG.8 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.286, B:A.303, B:D.313, B:D.313 Water bridges: A:R.286, A:R.286, A:R.286, A:R.286, A:K.287, A:K.287, B:K.307, B:K.307, B:K.307, B:K.307, B:K.307 Salt bridges: A:R.286, A:K.287, B:K.307 SO4.18: 10 residues within 4Å: Chain A: D.156 Chain B: H.51, D.53, K.203, D.280, K.287 Ligands: MTA.15, SO4.19, MG.20, MG.21 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Water bridges: B:K.203, B:K.287, A:K.307, A:K.307, A:K.307 Salt bridges: B:H.51, B:K.203, B:K.287 Hydrogen bonds: A:D.156, A:D.156 SO4.19: 11 residues within 4Å: Chain A: G.301, G.302, A.303, K.307, D.313 Chain B: D.53, R.286, K.287 Ligands: SO4.18, MG.20, MG.21 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:A.303, A:D.313, A:D.313, B:R.286 Water bridges: A:K.307, A:K.307, A:K.307, A:K.307, A:K.307, B:R.286, B:R.286, B:R.286, B:R.286, B:K.287, B:K.287 Salt bridges: A:K.307, B:R.286, B:K.287

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 7 residues within 4Å: Chain A: H.51, D.53, R.286, K.287 Ligands: SO4.5, SO4.6, K.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.53, H2O.2, H2O.2, H2O.2 MG.8: 6 residues within 4Å: Chain A: K.203, K.287 Chain B: G.302, D.313 Ligands: SO4.5, SO4.6 No protein-ligand interaction detected (PLIP) MG.20: 7 residues within 4Å: Chain B: H.51, D.53, R.286, K.287 Ligands: SO4.18, SO4.19, K.22 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.53, H2O.16, H2O.16, H2O.16 MG.21: 6 residues within 4Å: Chain A: G.302, D.313 Chain B: K.203, K.287 Ligands: SO4.18, SO4.19 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: D.280, A.281 Chain B: E.79 Ligands: MG.7 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.280, A:A.281, B:E.79, H2O.2, H2O.17 K.22: 4 residues within 4Å: Chain A: E.79 Chain B: D.280, A.281 Ligands: MG.20 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.280, B:A.281, A:E.79, H2O.3, H2O.16

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

NA.10: 5 residues within 4Å: Chain A: D.71, A.74, S.95, R.96 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.71, A:R.96 NA.11: 8 residues within 4Å: Chain A: F.42, G.295, W.296, G.297 Chain B: A.298, L.337 Ligands: P3G.3, P3G.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.295 Water bridges: A:G.297, A:G.297 NA.12: 4 residues within 4Å: Chain A: W.322, L.386, P.408, V.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.322, A:P.408 NA.13: 6 residues within 4Å: Chain A: M.160, H.299, G.302, F.304, D.313, A.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.302 Water bridges: A:G.300, A:G.302 NA.23: 5 residues within 4Å: Chain B: D.71, A.74, S.95, R.96 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.71, B:R.96 NA.24: 8 residues within 4Å: Chain A: A.298, L.337 Chain B: F.42, G.295, W.296, G.297 Ligands: P3G.3, P3G.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.297 Water bridges: B:G.297, B:G.297 NA.25: 4 residues within 4Å: Chain B: W.322, L.386, P.408, V.411 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.322, B:P.408 NA.26: 6 residues within 4Å: Chain B: M.160, H.299, G.302, F.304, D.313, A.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.313 Water bridges: B:G.300, B:G.302

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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