SMTL ID : 7loo.1

S-adenosyl methionine transferase cocrystallized with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

POP.1: 14 residues within 4Å: Chain A: H.15, D.17, K.166, D.239, R.245, K.246 Chain C: D.119, K.266, D.272 Ligands: PO4.2, MG.3, K.4, SAM.8, MG.21 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A Water bridges: C:D.119, C:K.266, C:D.272, C:D.272, A:K.166, A:K.166, A:K.166 Salt bridges: C:K.266, A:H.15, A:K.166, A:K.246, A:K.246 Hydrogen bonds: A:R.245 POP.11: 12 residues within 4Å: Chain B: H.15, D.17, K.166, D.239, R.245, K.246 Chain D: D.119, K.266, D.272 Ligands: MG.13, SAM.17, MG.32 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.245, D:D.119, D:D.272 Water bridges: B:K.166, B:K.246, B:K.246 Salt bridges: B:H.15, B:K.166, B:K.246, D:K.266 POP.18: 14 residues within 4Å: Chain A: D.119, K.266, D.272 Chain C: H.15, D.17, K.166, D.239, R.245, K.246 Ligands: MG.10, PO4.19, K.22, SAM.27, MG.29 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:D.272, C:R.245 Water bridges: A:K.266, A:K.266, C:K.166, C:K.166, C:K.166 Salt bridges: A:K.266, C:H.15, C:K.166, C:K.246, C:K.246 POP.31: 12 residues within 4Å: Chain B: D.119, K.266, D.272 Chain D: H.15, D.17, K.166, D.239, R.245, K.246 Ligands: MG.14, MG.33, SAM.34 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain D Hydrogen bonds: B:D.119, B:D.272, D:R.245 Salt bridges: B:K.266, D:H.15, D:K.166, D:K.246, D:K.246 Water bridges: D:K.166, D:K.246, D:K.246

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

PO4.2: 11 residues within 4Å: Chain A: D.17, R.245, K.246 Chain C: G.260, G.261, A.262, K.266, D.272 Ligands: POP.1, MG.3, MG.21 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.262 Water bridges: C:E.43, C:D.272, C:D.272, A:R.245 Salt bridges: C:K.266, A:R.245, A:K.246 PO4.12: 8 residues within 4Å: Chain A: I.65, E.66, V.92, L.93, S.94 Chain B: S.94, A.95, I.96 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.66, A:V.92, A:S.94, B:I.96, B:I.96 Water bridges: A:I.65 PO4.19: 11 residues within 4Å: Chain A: G.260, G.261, A.262, K.266, D.272 Chain C: D.17, R.245, K.246 Ligands: MG.10, POP.18, MG.29 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.262 Salt bridges: A:K.266, C:R.245, C:K.246 PO4.20: 8 residues within 4Å: Chain C: I.65, E.66, V.92, L.93, S.94 Chain D: S.94, A.95, I.96 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.66, C:V.92, C:S.94, D:I.96, D:I.96 Water bridges: C:I.65, C:I.65

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.17, K.246 Ligands: POP.1, PO4.2, K.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.17, H2O.1, H2O.2 MG.10: 3 residues within 4Å: Chain A: D.272 Ligands: POP.18, PO4.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.272, H2O.3, H2O.5 MG.13: 3 residues within 4Å: Chain B: D.17, K.246 Ligands: POP.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.17, H2O.10, H2O.10, H2O.11 MG.14: 6 residues within 4Å: Chain B: G.260, G.261, K.266, D.272 Chain D: K.246 Ligands: POP.31 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.272, H2O.10, H2O.23, H2O.23 MG.21: 3 residues within 4Å: Chain C: D.272 Ligands: POP.1, PO4.2 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.272, H2O.15, H2O.18 MG.29: 5 residues within 4Å: Chain C: D.17, K.246 Ligands: POP.18, PO4.19, K.22 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.17, H2O.14, H2O.14 MG.32: 6 residues within 4Å: Chain B: K.246 Chain D: G.260, G.261, K.266, D.272 Ligands: POP.11 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.272, H2O.10, H2O.11 MG.33: 3 residues within 4Å: Chain D: D.17, K.246 Ligands: POP.31 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.17, H2O.22, H2O.23, H2O.23

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: D.239, C.240 Chain C: E.43 Ligands: POP.1, MG.3, SAM.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.13, H2O.14 K.5: 3 residues within 4Å: Chain A: Y.126, R.294, F.316 No protein-ligand interaction detected (PLIP) K.22: 5 residues within 4Å: Chain A: E.43 Chain C: D.239, C.240 Ligands: POP.18, MG.29 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.239 K.23: 2 residues within 4Å: Chain C: Y.126, R.294 No protein-ligand interaction detected (PLIP)

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

EDO.6: 8 residues within 4Å: Chain A: E.66, R.70, A.91, V.92 Chain B: A.95, G.97 Chain D: K.47, T.48 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.66, A:R.70, A:V.92, D:T.48 EDO.7: 7 residues within 4Å: Chain A: S.94, A.95, I.96 Chain B: E.66, V.92, S.94 Ligands: SAM.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.92, B:S.94, A:I.96 EDO.15: 8 residues within 4Å: Chain A: A.95, I.96, G.97 Chain B: E.66, R.70, A.91, V.92 Chain C: T.48 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.66, B:R.70, B:V.92, C:T.48 Water bridges: C:T.48, A:K.98 EDO.16: 2 residues within 4Å: Chain B: A.61, V.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.61 EDO.24: 3 residues within 4Å: Chain C: K.37, Q.343, L.348 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.343, C:Q.343 EDO.25: 6 residues within 4Å: Chain C: E.13, Q.147, A.150, E.151, K.154, Y.358 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain C: Y.281, M.344, P.367, D.372 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.281, C:D.372 EDO.30: 7 residues within 4Å: Chain C: S.94, I.96 Chain D: E.66, V.92, L.93, S.94 Ligands: SAM.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.92 EDO.35: 8 residues within 4Å: Chain A: T.48 Chain C: A.95, I.96, G.97 Chain D: E.66, R.70, A.91, V.92 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.70, D:V.92, D:V.92 Water bridges: D:E.66, C:K.98

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

SAM.8: 20 residues within 4Å: Chain A: H.15, P.16, D.164, K.166, S.187, T.228, R.230, F.231, G.238, D.239 Chain C: A.41, E.56, Q.99, D.102, I.103, D.119, K.270, I.303 Ligands: POP.1, K.4 21 PLIP interactions: 9 interactions with chain C, 12 interactions with chain A Hydrogen bonds: C:E.56, C:Q.99, A:D.164, A:S.187, A:T.228, A:T.228, A:D.239, A:D.239, A:D.239 Water bridges: C:I.103, C:Q.120, C:K.270, C:K.270, C:K.270, A:R.230, A:C.240 Salt bridges: C:D.119, C:K.270, A:D.239 pi-Stacking: A:F.231, A:F.231 SAM.9: 10 residues within 4Å: Chain A: I.57, T.58, T.59, S.60, A.61, V.63, I.65, G.97, K.98 Ligands: EDO.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.57, A:T.59, A:T.59, A:V.63, A:V.63, A:I.65 SAM.17: 19 residues within 4Å: Chain B: H.15, P.16, D.164, K.166, S.187, T.228, R.230, F.231, D.239 Chain D: A.41, E.56, Q.99, D.102, I.103, G.118, D.119, K.270, I.303 Ligands: POP.11 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:D.164, B:T.228, B:D.239, B:D.239, D:E.56, D:E.56 Water bridges: B:C.240, D:K.270, D:K.270 Salt bridges: B:D.239, D:D.119, D:K.270 pi-Stacking: B:F.231, B:F.231 SAM.27: 19 residues within 4Å: Chain A: A.41, E.56, Q.99, D.102, I.103, D.119, K.270, I.303 Chain C: H.15, P.16, D.164, K.166, S.187, T.228, R.230, F.231, G.238, D.239 Ligands: POP.18 21 PLIP interactions: 11 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:D.164, C:K.166, C:S.187, C:T.228, C:T.228, C:D.239, A:E.56, A:E.56, A:E.56, A:Q.99 Water bridges: C:R.230, C:C.240, A:I.103, A:I.103, A:K.270, A:K.270 Salt bridges: C:D.239, A:D.119, A:K.270 pi-Stacking: C:F.231, C:F.231 SAM.28: 11 residues within 4Å: Chain C: I.57, T.58, T.59, S.60, A.61, W.62, V.63, I.65, G.97, K.98 Ligands: EDO.30 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:I.57, C:T.59, C:T.59, C:V.63, C:V.63 Water bridges: C:T.59, C:I.65 SAM.34: 19 residues within 4Å: Chain B: A.41, E.56, Q.99, D.102, I.103, D.119, K.270, I.303 Chain D: H.15, P.16, D.164, K.166, S.187, T.228, R.230, F.231, G.238, D.239 Ligands: POP.31 14 PLIP interactions: 7 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:D.164, D:S.187, D:T.228, D:D.239, B:E.56, B:E.56, B:Q.99 Salt bridges: D:D.239, B:D.119, B:K.270 pi-Stacking: D:F.231, D:F.231 Water bridges: B:K.270, B:K.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gade, M. et al., Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. Jacs Au (2021)

Release Date

2021-09-15

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
Q

D
R

S-adenosylmethionine synthase

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