SMTL ID : 7l1a.1

Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine and inhibitor, di-imido triphosphate (PNPNP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: H.51, D.53, R.286, K.287 Ligands: K.3, XE1.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, H2O.2, H2O.2 MG.2: 5 residues within 4Å: Chain A: K.203, K.287 Chain B: G.302, D.313 Ligands: XE1.4 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain B: H.51, D.53, R.286, K.287 Ligands: K.15, XE1.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.53, H2O.15, H2O.15 MG.14: 5 residues within 4Å: Chain A: G.302, D.313 Chain B: K.203, K.287 Ligands: XE1.16 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.280, A.281 Chain B: E.79 Ligands: MG.1, XE1.4 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.15 K.15: 5 residues within 4Å: Chain A: E.79 Chain B: D.280, A.281 Ligands: MG.13, XE1.16 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.1

2 x XE1: N,N'-(dihydroxy-lambda~5~-phosphanediyl)bis(phosphoramidic acid)(Non-covalent)

XE1.4: 18 residues within 4Å: Chain A: H.51, D.53, K.203, D.280, R.286, K.287 Chain B: E.79, D.156, G.301, G.302, A.303, K.307, D.313 Ligands: MG.1, MG.2, K.3, MTA.5, ALA.6 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:H.51, A:K.203, A:D.280, A:D.280, A:R.286, A:R.286, A:K.287, B:D.156, B:A.303, B:K.307, B:D.313, B:D.313 Water bridges: B:D.156, B:D.156, B:D.156, B:D.156 XE1.16: 18 residues within 4Å: Chain A: E.79, D.156, G.301, G.302, A.303, K.307, D.313 Chain B: H.51, D.53, K.203, D.280, R.286, K.287 Ligands: MG.13, MG.14, K.15, MTA.17, ALA.18 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.156, A:A.303, A:K.307, A:D.313, A:D.313, B:H.51, B:D.53, B:K.203, B:D.280, B:D.280, B:R.286, B:R.286, B:K.287 Water bridges: A:D.156, A:D.156, A:D.156, A:D.156

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

MTA.5: 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: XE1.4, ALA.6 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.201, A:S.269, A:R.271 Water bridges: A:S.228, A:S.269, B:I.139, B:I.139 pi-Stacking: A:F.272, A:F.272 MTA.17: 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: XE1.16, ALA.18 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.201, B:S.269, B:R.271 Water bridges: B:S.228, B:S.269, A:I.139, A:I.139 pi-Stacking: B:F.272, B:F.272

2 x ALA: ALANINE(Non-covalent)

ALA.6: 8 residues within 4Å: Chain A: D.280 Chain B: A.77, E.92, Q.135, I.139, K.311 Ligands: XE1.4, MTA.5 9 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A.6, B:E.92, B:E.92 Water bridges: A:A.281, B:K.311, B:K.311, B:K.311, B:K.311 Salt bridges: B:K.311 ALA.18: 8 residues within 4Å: Chain A: A.77, E.92, Q.135, I.139, K.311 Chain B: D.280 Ligands: XE1.16, MTA.17 10 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.92, A:E.92, B:D.280, A.18 Water bridges: A:K.311, A:K.311, A:K.311, A:K.311, B:A.281 Salt bridges: A:K.311

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

NA.7: 3 residues within 4Å: Chain A: I.220, K.256, Y.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.220 NA.8: 2 residues within 4Å: Chain A: H.111, R.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.111, A:R.191 Water bridges: A:R.191 NA.9: 4 residues within 4Å: Chain A: D.166, T.168, E.169, K.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.166, A:K.329 NA.10: 2 residues within 4Å: Chain A: D.232, E.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.233 NA.11: 5 residues within 4Å: Chain A: I.289, Y.293, G.294, G.295, W.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.295, A:G.295 Water bridges: A:Y.293 NA.12: 2 residues within 4Å: Chain A: D.405, S.406 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.405, A:S.406 Water bridges: A:S.406 NA.19: 3 residues within 4Å: Chain B: I.220, K.256, Y.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.220 NA.20: 2 residues within 4Å: Chain B: H.111, R.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.111, B:R.191 Water bridges: B:R.191 NA.21: 4 residues within 4Å: Chain B: D.166, T.168, E.169, K.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.166, B:K.329 NA.22: 2 residues within 4Å: Chain B: D.232, E.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.233 NA.23: 5 residues within 4Å: Chain B: I.289, Y.293, G.294, G.295, W.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.295, B:G.295 Water bridges: B:Y.293 NA.24: 2 residues within 4Å: Chain B: D.405, S.406 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.405, B:S.406 Water bridges: B:S.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niland, C.N. et al., Mechanism and Inhibition of Human Methionine Adenosyltransferase 2A. Biochemistry (2021)

Release Date

2021-03-17

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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