SMTL ID : 8jzg.1

C. glutamicum S-adenosylmethionine synthase co-crystallized with Adenosine, triphosphate, and SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 13 residues within 4Å: Chain A: H.19, P.20, D.178, K.180, S.202, S.247, G.248, S.249, F.250, D.258 Chain B: D.133, I.322 Ligands: 3PO.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.178, A:S.202, A:G.248, A:D.258 pi-Stacking: A:F.250 ADN.10: 11 residues within 4Å: Chain A: D.133, I.322 Chain B: H.19, P.20, D.178, K.180, S.202, S.247, S.249, F.250, D.258 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.178, B:S.247, B:D.258 pi-Stacking: B:F.250 ADN.16: 10 residues within 4Å: Chain C: H.19, P.20, D.178, K.180, S.202, S.247, S.249, F.250, D.258 Chain D: I.322 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.178, C:S.202, C:S.247, C:D.258 pi-Stacking: C:F.250, C:F.250 ADN.22: 13 residues within 4Å: Chain C: D.133, I.322 Chain D: H.19, P.20, D.178, K.180, S.202, S.247, G.248, S.249, F.250, D.258 Ligands: 3PO.23 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.178, D:G.248, D:D.258 pi-Stacking: D:F.250, D:F.250

4 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.2: 14 residues within 4Å: Chain A: H.19, D.21, K.180, R.264, K.265 Chain B: D.133, G.280, A.281, K.285, D.291 Ligands: ADN.1, MG.6, K.8, MG.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Water bridges: A:K.180 Salt bridges: A:H.19, A:K.180, A:R.264, A:K.265, A:K.265, A:K.265, B:K.285, B:K.285 Hydrogen bonds: B:D.133, B:A.281 3PO.11: 14 residues within 4Å: Chain A: D.133, G.279, G.280, A.281, K.285, D.291 Chain B: H.19, D.21, K.180, R.264, K.265 Ligands: MG.7, K.9, MG.15 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.264, A:A.281 Water bridges: B:K.180, B:K.180, B:K.180 Salt bridges: B:H.19, B:K.180, B:R.264, B:K.265, B:K.265, A:K.285, A:K.285 3PO.17: 14 residues within 4Å: Chain C: H.19, D.21, K.180, R.264, K.265 Chain D: D.133, G.279, G.280, A.281, K.285, D.291 Ligands: MG.19, MG.25, K.27 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:A.281, C:R.264 Salt bridges: D:K.285, D:K.285, C:H.19, C:K.180, C:R.264, C:K.265, C:K.265 3PO.23: 15 residues within 4Å: Chain C: D.133, G.279, G.280, A.281, K.285, D.291 Chain D: H.19, D.21, K.180, R.264, K.265 Ligands: MG.20, K.21, ADN.22, MG.26 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.264, C:G.279, C:A.281 Water bridges: D:K.180 Salt bridges: D:H.19, D:K.180, D:R.264, D:K.265, D:K.265, D:K.265, C:K.285, C:K.285

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

SAM.3: 12 residues within 4Å: Chain A: V.61, R.62, T.63, S.64, A.65, Y.66, V.67, I.69, I.100, G.101 Chain D: Y.66, E.68 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:V.61, A:T.63, A:T.63, A:V.67, A:V.67, D:Y.66 pi-Stacking: D:Y.66 pi-Cation interactions: D:Y.66 SAM.12: 11 residues within 4Å: Chain B: V.61, R.62, T.63, S.64, A.65, Y.66, V.67, I.69, G.101, Q.103 Chain C: Y.66 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.61, B:T.63, B:T.63, B:V.67, B:V.67 Water bridges: C:Y.66 pi-Cation interactions: C:Y.66 SAM.18: 13 residues within 4Å: Chain B: Y.66, E.68 Chain C: V.61, R.62, T.63, S.64, A.65, Y.66, V.67, I.69, G.101, E.102, Q.103 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:Y.66 Hydrogen bonds: B:Y.66, C:V.61, C:T.63, C:T.63, C:S.64, C:V.67, C:V.67 pi-Stacking: B:Y.66 pi-Cation interactions: B:Y.66 SAM.24: 13 residues within 4Å: Chain A: Y.66, E.68 Chain D: V.61, R.62, T.63, S.64, A.65, Y.66, V.67, I.69, I.100, G.101, Q.103 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:V.61, D:T.63, D:T.63, D:V.67, D:V.67, A:Y.66 Water bridges: D:I.69, A:Y.66 Salt bridges: A:K.38 pi-Cation interactions: A:Y.66

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: E.17, A.26, K.76, A.374, D.375, A.378, Y.379 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76 GOL.13: 7 residues within 4Å: Chain B: E.17, A.26, K.76, I.80, A.374, D.375, A.378 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.17, B:K.76, B:D.375 Water bridges: B:D.375

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 8 residues within 4Å: Chain A: H.56, S.97 Chain B: H.56, S.97 Chain C: H.56, S.97 Chain D: H.56, S.97 15 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:S.97, D:S.97, A:S.97, A:S.97, B:S.97, B:S.97, C:S.97 Salt bridges: D:H.56, D:H.56, A:H.56, A:H.56, B:H.56, B:H.56, C:H.56, C:H.56

8 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: D.21, R.264 Ligands: 3PO.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.21 MG.7: 2 residues within 4Å: Chain A: D.291 Ligands: 3PO.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.291, H2O.1 MG.14: 3 residues within 4Å: Chain B: D.133, D.291 Ligands: 3PO.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.291 MG.15: 3 residues within 4Å: Chain B: D.21, K.265 Ligands: 3PO.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.21 MG.19: 4 residues within 4Å: Chain C: D.21, R.264, K.265 Ligands: 3PO.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.21 MG.20: 3 residues within 4Å: Chain C: D.133, D.291 Ligands: 3PO.23 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.291 MG.25: 3 residues within 4Å: Chain D: D.133, D.291 Ligands: 3PO.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.291 MG.26: 3 residues within 4Å: Chain D: D.21, K.265 Ligands: 3PO.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.21

4 x K: POTASSIUM ION(Non-covalent)

K.8: 4 residues within 4Å: Chain A: D.258, A.259 Chain B: E.60 Ligands: 3PO.2 No protein-ligand interaction detected (PLIP) K.9: 4 residues within 4Å: Chain A: E.60 Chain B: D.258, A.259 Ligands: 3PO.11 No protein-ligand interaction detected (PLIP) K.21: 4 residues within 4Å: Chain C: E.60 Chain D: D.258, A.259 Ligands: 3PO.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.258 K.27: 4 residues within 4Å: Chain C: D.258, A.259 Chain D: E.60 Ligands: 3PO.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S. et al., Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum . J.Agric.Food Chem. (2023)

Release Date

2023-10-25

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosylmethionine synthase