SMTL ID : 7r2w.1

Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: H.15, P.16, D.17, D.164, K.166, T.228, R.230, F.231, D.239, R.245, K.246 Chain C: E.43, D.119, G.261, A.262, K.266, D.272, I.303 Ligands: MG.2, MG.3, K.4 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:D.164, A:R.230, A:D.239, A:R.245, A:R.245, C:D.119, C:A.262, C:K.266, C:K.266, C:D.272 Water bridges: A:K.166, A:T.228 Salt bridges: A:H.15, A:K.166, A:K.246 pi-Stacking: A:F.231, A:F.231 ANP.5: 21 residues within 4Å: Chain B: H.15, P.16, D.17, D.164, K.166, T.228, R.230, F.231, D.239, R.245, K.246 Chain D: E.43, D.119, G.261, A.262, K.266, D.272, I.303 Ligands: MG.6, MG.7, K.8 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:D.164, B:R.230, B:D.239, B:R.245, B:R.245, D:D.119, D:A.262, D:K.266, D:K.266, D:D.272 Water bridges: B:K.166, B:T.228 Salt bridges: B:H.15, B:K.166, B:K.246 pi-Stacking: B:F.231, B:F.231 ANP.9: 21 residues within 4Å: Chain A: E.43, D.119, G.261, A.262, K.266, D.272, I.303 Chain C: H.15, P.16, D.17, D.164, K.166, T.228, R.230, F.231, D.239, R.245, K.246 Ligands: MG.10, MG.11, K.12 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.164, C:T.228, C:R.230, C:D.239, C:D.239, C:R.245, C:R.245, A:A.262, A:K.266, A:K.266 Water bridges: C:K.166 Salt bridges: C:H.15, C:K.166, C:K.246 pi-Stacking: C:F.231, C:F.231 ANP.13: 21 residues within 4Å: Chain B: E.43, D.119, G.261, A.262, K.266, D.272, I.303 Chain D: H.15, P.16, D.17, D.164, K.166, T.228, R.230, F.231, D.239, R.245, K.246 Ligands: MG.14, MG.15, K.16 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:D.164, D:T.228, D:R.230, D:D.239, D:D.239, D:R.245, D:R.245, B:E.43, B:E.43, B:A.262, B:K.266, B:K.266 Water bridges: D:K.166 Salt bridges: D:H.15, D:K.166, D:K.246 pi-Stacking: D:F.231, D:F.231

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain C: D.272 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.17, R.245, K.246 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.17, H2O.2, H2O.2 MG.6: 2 residues within 4Å: Chain D: D.272 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: D.17, R.245, K.246 Ligands: ANP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.17, H2O.9, H2O.9 MG.10: 2 residues within 4Å: Chain A: D.272 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.17, R.245, K.246 Ligands: ANP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.17, H2O.16, H2O.16 MG.14: 2 residues within 4Å: Chain B: D.272 Ligands: ANP.13 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: D.17, R.245, K.246 Ligands: ANP.13 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.17, H2O.23, H2O.23

4 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: D.239, C.240 Chain C: E.43 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.43 K.8: 4 residues within 4Å: Chain B: D.239, C.240 Chain D: E.43 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.43 K.12: 4 residues within 4Å: Chain A: E.43 Chain C: D.239, C.240 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.43 K.16: 4 residues within 4Å: Chain B: E.43 Chain D: D.239, C.240 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kleiner, D. et al., Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Protein Sci. (2022)

Release Date

2022-07-13

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-adenosylmethionine synthase