SMTL ID : 6vd1.1

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine and PPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.1: 16 residues within 4Å: Chain A: H.18, D.20, K.172, D.249, R.255, K.256 Chain B: E.46, D.125, G.271, A.272, K.276, D.282 Ligands: MG.2, MG.3, K.5, SAM.9 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.255, A:R.255, A:K.256, B:G.270, B:A.272, B:K.276, B:K.276, B:K.276 Water bridges: A:K.172, B:D.125, B:D.125, B:D.125, B:D.125 Salt bridges: A:H.18, A:K.172, A:K.256 PPK.11: 15 residues within 4Å: Chain A: D.125, G.271, A.272, K.276, D.282 Chain B: H.18, D.20, K.172, D.249, R.255, K.256 Ligands: MG.4, MG.14, K.16, SAM.19 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.249, B:R.255, B:K.256, A:A.272, A:K.276, A:K.276 Water bridges: B:D.20, B:D.20, B:K.172 Salt bridges: B:H.18, B:K.172, B:K.256

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.20, K.256 Ligands: PPK.1, K.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, H2O.3, H2O.4 MG.3: 3 residues within 4Å: Chain A: K.256 Chain B: D.282 Ligands: PPK.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: D.282 Chain B: K.256 Ligands: PPK.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain B: D.20, K.256 Ligands: PPK.11, K.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.20, H2O.26, H2O.26

2 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: D.249, A.250 Chain B: E.46 Ligands: PPK.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.249, A:A.250, B:E.46, H2O.28 K.16: 5 residues within 4Å: Chain A: E.46 Chain B: D.249, A.250 Ligands: PPK.11, MG.14 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.249, B:A.250, A:E.46, H2O.5

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

MPO.6: 9 residues within 4Å: Chain A: D.40, K.42, H.111, F.114, T.115, K.116, R.117, I.121, K.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.111 Water bridges: A:K.358, A:K.358 Salt bridges: A:K.42, A:K.358 MPO.17: 9 residues within 4Å: Chain B: D.40, K.42, H.111, F.114, T.115, K.116, R.117, I.121, K.358 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.358, B:K.358, B:K.358 Salt bridges: B:K.42, B:K.358

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 6 residues within 4Å: Chain A: K.341, E.342, T.343, F.344, D.345, R.347 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.346

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

PGE.8: 4 residues within 4Å: Chain A: K.94, L.96 Chain B: V.97, N.98 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.98 Hydrogen bonds: A:K.94 PGE.18: 2 residues within 4Å: Chain B: N.161, R.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.165 Water bridges: B:N.161, B:R.165

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.9: 19 residues within 4Å: Chain A: H.18, P.19, D.170, K.172, S.238, R.240, F.241, I.243, D.249 Chain B: A.44, E.59, Q.102, D.105, I.106, G.124, D.125, K.280, I.313 Ligands: PPK.1 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.170, A:S.238, A:R.240, A:D.249, B:E.59, B:E.59, B:Q.102 Water bridges: A:S.197, A:S.238, A:A.250, B:K.280, B:K.280, B:K.280 Salt bridges: A:D.249, B:D.125, B:K.280 pi-Stacking: A:F.241, A:F.241 SAM.19: 19 residues within 4Å: Chain A: A.44, E.59, Q.102, D.105, I.106, G.124, D.125, K.280, I.313 Chain B: H.18, P.19, D.170, K.172, S.238, R.240, F.241, I.243, D.249 Ligands: PPK.11 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:E.59, A:Q.102, B:D.170, B:S.238, B:R.240, B:D.249 Water bridges: A:D.125, A:K.280, A:K.280, A:K.280, B:S.197, B:S.238, B:A.250 Salt bridges: A:D.125, A:K.280, B:D.249 pi-Stacking: B:F.241, B:F.241

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

EDO.10: 2 residues within 4Å: Chain A: E.202, T.205 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.202 EDO.20: 3 residues within 4Å: Chain B: M.4, V.187, P.188 No protein-ligand interaction detected (PLIP)

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.12: 4 residues within 4Å: Chain B: K.214, K.219, E.224, L.227 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.227 Hydrogen bonds: B:K.214, B:K.214, B:E.224

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

PGR.13: 5 residues within 4Å: Chain B: T.149, K.150, A.153, Y.371, R.376 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.153 Hydrogen bonds: B:Y.371

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.15: 20 residues within 4Å: Chain A: F.7, F.9, N.181, M.186, G.264, W.265, A.267, L.306, F.322, D.324 Chain B: F.7, F.9, N.181, M.186, G.264, W.265, A.267, R.304, L.306, D.324 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.264, B:G.264 Water bridges: A:G.266, A:R.304, A:R.304, A:D.324, B:N.181, B:G.266, B:R.304, B:R.304, B:Y.326

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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