SMTL ID : 6vcz.1

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: H.18, D.20, K.172, K.256 Chain B: D.125 Ligands: PO4.2, MG.5, MG.6, MG.16 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Water bridges: A:K.172, A:K.172, A:R.255, B:D.125, B:D.125, B:D.125, B:D.282 Salt bridges: A:H.18, A:K.172, A:K.256 PO4.2: 10 residues within 4Å: Chain A: D.20, R.255, K.256 Chain B: G.271, A.272, K.276, D.282 Ligands: PO4.1, MG.5, MG.16 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:A.272 Water bridges: B:K.276, B:D.282, A:R.255, A:R.255, A:K.256 Salt bridges: B:K.276, A:R.255, A:K.256 PO4.3: 5 residues within 4Å: Chain A: K.172, S.197, F.241 Chain B: D.125, I.313 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.172 Hydrogen bonds: B:D.125 PO4.4: 4 residues within 4Å: Chain A: P.138, E.139, K.294, E.384 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.384 Water bridges: A:K.294, A:K.294, A:K.294 Salt bridges: A:K.294 PO4.9: 9 residues within 4Å: Chain A: D.125 Chain B: H.18, D.20, K.172, K.256 Ligands: MG.7, PO4.10, MG.13, MG.14 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Water bridges: A:D.125, A:D.282, B:K.172, B:K.172, B:K.172 Salt bridges: B:H.18, B:K.172, B:K.256 PO4.10: 10 residues within 4Å: Chain A: G.271, A.272, K.276, D.282 Chain B: D.20, R.255, K.256 Ligands: MG.7, PO4.9, MG.13 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.272 Water bridges: A:K.276, B:R.255, B:R.255 Salt bridges: A:K.276, B:R.255, B:K.256 PO4.11: 5 residues within 4Å: Chain A: D.125, I.313 Chain B: K.172, S.197, F.241 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:D.170, B:K.172, A:D.125, A:D.125 Salt bridges: B:K.172 PO4.12: 2 residues within 4Å: Ligands: MG.15, MPO.17 No protein-ligand interaction detected (PLIP)

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 5 residues within 4Å: Chain A: D.20, R.255, K.256 Ligands: PO4.1, PO4.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.20, H2O.4, H2O.8, H2O.8 MG.6: 3 residues within 4Å: Chain A: D.249 Chain B: D.125 Ligands: PO4.1 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: K.276, D.282 Ligands: PO4.9, PO4.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.282, H2O.5, H2O.9, H2O.20 MG.13: 4 residues within 4Å: Chain B: D.20, K.256 Ligands: PO4.9, PO4.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.20, H2O.24, H2O.27, H2O.28 MG.14: 2 residues within 4Å: Chain A: D.125 Ligands: PO4.9 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: PO4.12 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain B: K.276, D.282 Ligands: PO4.1, PO4.2 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.282, H2O.1, H2O.24, H2O.30

2 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.8: 6 residues within 4Å: Chain A: T.137, P.138, E.139, V.146, K.150, P.223 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.226 PGR.19: 7 residues within 4Å: Chain B: T.137, P.138, E.139, L.143, V.146, K.150, P.223 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.150

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.17: 5 residues within 4Å: Chain B: D.67, E.69, K.70, R.73 Ligands: PO4.12 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.67, B:K.70, B:R.73 Salt bridges: B:D.67

1 x MXE: 2-METHOXYETHANOL(Non-covalent)

MXE.18: 3 residues within 4Å: Chain B: E.202, T.203, T.205 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.240, B:R.240, B:R.240

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.20: 10 residues within 4Å: Chain A: F.7, F.9, Y.132, N.181, M.186, W.265, G.266, R.304, Y.326 Chain B: D.324 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.181, A:G.266, A:R.304 Water bridges: A:N.181, B:D.324, B:D.324 PGE.21: 12 residues within 4Å: Chain A: G.266, A.267, F.322, D.324 Chain B: F.7, F.9, N.181, M.186, G.264, W.265, G.266, R.304 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:D.324, B:G.266 Hydrogen bonds: B:G.264, B:R.304, B:R.304

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 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase 2

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