SMTL ID : 4k0b.1

Crystal structure of S-Adenosylmethionine synthetase from Sulfolobus solfataricus complexed with SAM and PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.308 Ligands: DPO.3, PO4.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.308, A:E.308, H2O.1 MG.2: 4 residues within 4Å: Chain B: K.28, D.34 Ligands: DPO.3, PO4.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.34, H2O.18, H2O.18 MG.6: 3 residues within 4Å: Chain C: E.308 Ligands: DPO.8, PO4.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.308, C:E.308, H2O.23 MG.7: 4 residues within 4Å: Chain D: K.28, D.34 Ligands: DPO.8, PO4.9 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.34, H2O.41, H2O.41

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.3: 16 residues within 4Å: Chain A: D.65, K.66, D.163, E.308, K.313, H.318 Chain B: K.28, H.32, D.34, K.204, D.285, R.291 Ligands: MG.1, MG.2, PO4.4, SAM.5 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:E.308, B:D.285, B:R.291 Water bridges: A:K.66, A:K.66, A:K.66, A:D.163, A:D.163 Salt bridges: A:K.66, A:K.313, A:H.318, B:K.28, B:K.28, B:H.32, B:K.204 DPO.8: 16 residues within 4Å: Chain C: D.65, K.66, D.163, E.308, K.313, H.318 Chain D: K.28, H.32, D.34, K.204, D.285, R.291 Ligands: MG.6, MG.7, PO4.9, SAM.10 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:E.308, D:D.285, D:R.291 Water bridges: C:K.66, C:K.66, C:K.66 Salt bridges: C:K.66, C:K.313, C:H.318, D:K.28, D:K.28, D:H.32, D:K.204

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

PO4.4: 10 residues within 4Å: Chain A: L.307, E.308, A.309, K.313 Chain B: K.28, D.34, R.291 Ligands: MG.1, MG.2, DPO.3 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Salt bridges: B:K.28, B:R.291, A:K.313 Hydrogen bonds: A:L.307, A:A.309 Water bridges: A:K.66, A:K.66 PO4.9: 10 residues within 4Å: Chain C: L.307, E.308, A.309, K.313 Chain D: K.28, D.34, R.291 Ligands: MG.6, MG.7, DPO.8 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:L.307, C:A.309 Water bridges: C:K.66, C:K.66, C:E.308 Salt bridges: C:K.313, D:K.28, D:R.291

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

SAM.5: 18 residues within 4Å: Chain A: H.61, N.63, R.94, D.147, L.148, N.162, D.163, I.352 Chain B: H.32, P.33, D.202, K.204, A.219, Y.273, S.280, G.284, D.285 Ligands: DPO.3 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:N.63, A:D.147, A:N.162, A:N.162, B:D.202, B:K.204, B:Y.273, B:S.280, B:D.285, B:D.285, B:D.285 Water bridges: A:K.66, A:S.145 Salt bridges: A:H.61, A:D.163, B:D.285 pi-Stacking: B:Y.273, B:Y.273 SAM.10: 18 residues within 4Å: Chain C: H.61, N.63, R.94, D.147, L.148, N.162, D.163, I.352 Chain D: H.32, P.33, D.202, K.204, A.219, Y.273, S.280, G.284, D.285 Ligands: DPO.8 18 PLIP interactions: 9 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:D.202, D:K.204, D:S.280, D:D.285, D:D.285, D:D.285, C:N.63, C:D.147, C:D.147, C:N.162, C:N.162 Salt bridges: D:D.285, C:H.61, C:D.163 pi-Stacking: D:Y.273, D:Y.273 Water bridges: C:K.66, C:S.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus. Febs J. (2014)

Release Date

2013-05-01

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-adenosylmethionine synthase

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