SMTL ID : 6vcx.1

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1 (AtMAT1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: D.20, R.255, K.256 Chain B: G.271, A.272, K.276, D.282 Ligands: SO4.3, MG.4 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:A.272, B:D.282 Salt bridges: B:K.276, A:R.255, A:K.256 Water bridges: A:K.256, A:K.256, A:K.256, A:K.256 SO4.2: 3 residues within 4Å: Chain A: I.222, P.223, E.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.224 Water bridges: A:K.225 SO4.3: 7 residues within 4Å: Chain A: H.18, D.20, K.172, K.256 Chain B: D.125 Ligands: SO4.1, MG.4 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.125, B:D.125 Water bridges: A:K.172, A:K.172, A:K.172, A:K.256, A:K.256, A:K.256 Salt bridges: A:H.18, A:K.172, A:K.256 SO4.15: 9 residues within 4Å: Chain A: G.271, A.272, K.276, D.282 Chain B: D.20, R.255, K.256 Ligands: SO4.17, MG.18 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:K.256, B:K.256, B:K.256, B:K.256 Salt bridges: B:R.255, B:K.256, A:K.276 Hydrogen bonds: A:A.272, A:D.282 SO4.16: 3 residues within 4Å: Chain B: I.222, P.223, E.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.224 Water bridges: B:K.225 SO4.17: 7 residues within 4Å: Chain A: D.125 Chain B: H.18, D.20, K.172, K.256 Ligands: SO4.15, MG.18 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Water bridges: B:K.172, B:K.172, B:K.172, B:K.256, B:K.256, B:K.256 Salt bridges: B:H.18, B:K.172, B:K.256 Hydrogen bonds: A:D.125, A:D.125

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.20, K.256 Ligands: SO4.1, SO4.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.20, H2O.1, H2O.4, H2O.4, H2O.12 MG.5: 1 residues within 4Å: Chain A: D.67 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.67, H2O.5, H2O.12, H2O.14, H2O.16, H2O.20 MG.18: 4 residues within 4Å: Chain B: D.20, K.256 Ligands: SO4.15, SO4.17 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.20, H2O.21, H2O.25, H2O.25, H2O.33 MG.19: 1 residues within 4Å: Chain B: D.67 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.67, H2O.25, H2O.33, H2O.35, H2O.37, H2O.40

16 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: R.240, F.241, V.242, I.243 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: F.344, D.345, K.387 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: G.124, D.125, K.280, V.281 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.73, C.93, K.94, V.95 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: R.168, D.201, E.202, T.203 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: K.116, G.122 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: S.320, V.321, K.341 Chain B: L.8 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: T.61, P.104, D.105 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: R.240, F.241, V.242, I.243 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: F.344, D.345, K.387 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: G.124, D.125, K.280, V.281 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: R.73, C.93, K.94, V.95 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: R.168, D.201, E.202, T.203 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: K.116, G.122 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: L.8 Chain B: S.320, V.321, K.341 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: T.61, P.104, D.105 Ligand excluded by PLIP

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.14: 5 residues within 4Å: Chain A: E.16, Q.25, I.79, L.366, K.367 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.366 Water bridges: A:K.367, A:R.376, A:R.376 Salt bridges: A:E.16 BTB.28: 5 residues within 4Å: Chain B: E.16, Q.25, I.79, L.366, K.367 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.366 Water bridges: B:K.367, B:R.376, B:R.376 Salt bridges: B:E.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekula, B. et al., S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int.J.Biol.Macromol. (2020)

Release Date

2020-02-26

Peptides

S-adenosylmethionine synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-adenosylmethionine synthase 1

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