SMTL ID : 7lo2.1

S-adenosylmethionine synthetase cocrystallized with CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.17, K.246 Ligands: PO4.4, POP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, H2O.1, H2O.2, H2O.2 MG.2: 5 residues within 4Å: Chain A: R.245, K.246 Chain B: G.261 Ligands: PO4.4, POP.5 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: D.272 Ligands: PO4.15, POP.18 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.272, H2O.3, H2O.10 MG.14: 5 residues within 4Å: Chain B: D.17, K.246 Ligands: PO4.15, K.16, POP.18 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.17, H2O.8, H2O.10 MG.22: 4 residues within 4Å: Chain C: D.17, K.246 Ligands: POP.26, PO4.35 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.17, H2O.14, H2O.14 MG.23: 4 residues within 4Å: Chain C: K.246 Chain D: D.272 Ligands: POP.26, PO4.35 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain C: D.272 Ligands: PO4.36, POP.37 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.272, H2O.16, H2O.17 MG.34: 4 residues within 4Å: Chain D: D.17, K.246 Ligands: PO4.36, POP.37 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.17, H2O.20, H2O.22

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

PO4.4: 10 residues within 4Å: Chain A: D.17, R.245, K.246 Chain B: G.261, A.262, K.266, D.272 Ligands: MG.1, MG.2, POP.5 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Water bridges: A:R.245, B:G.261, B:G.261, B:K.266 Salt bridges: A:R.245, A:K.246, B:K.266 Hydrogen bonds: B:A.262, B:D.272 PO4.15: 11 residues within 4Å: Chain A: G.260, G.261, A.262, K.266, D.272 Chain B: D.17, R.245, K.246 Ligands: MG.3, MG.14, POP.18 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.262, A:D.272, A:D.272 Salt bridges: A:K.266, B:R.245, B:K.246 PO4.35: 10 residues within 4Å: Chain C: D.17, R.245, K.246 Chain D: G.261, A.262, K.266, D.272 Ligands: MG.22, MG.23, POP.26 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Water bridges: C:D.17, C:D.17, D:G.261, D:G.261, D:K.266 Salt bridges: C:R.245, C:K.246, D:K.266 Hydrogen bonds: D:A.262, D:D.272, D:D.272 PO4.36: 11 residues within 4Å: Chain C: G.260, G.261, A.262, K.266, D.272 Chain D: D.17, R.245, K.246 Ligands: MG.24, MG.34, POP.37 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.262, D:R.245 Water bridges: C:G.260, D:R.245 Salt bridges: C:K.266, D:R.245, D:K.246

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

POP.5: 9 residues within 4Å: Chain A: E.9, H.15, D.17, K.166, K.246 Chain B: D.272 Ligands: MG.1, MG.2, PO4.4 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.9 Water bridges: A:H.15, A:D.17, A:D.239, A:D.239, B:K.266, B:D.272 Salt bridges: A:H.15, A:K.166, A:K.246, A:K.246 POP.18: 12 residues within 4Å: Chain A: D.119, K.266, D.272 Chain B: H.15, D.17, K.166, R.245, K.246 Ligands: MG.3, MG.14, PO4.15, K.16 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.245, A:D.272 Water bridges: B:K.166, B:K.166, B:K.166, A:K.266, A:K.266 Salt bridges: B:H.15, B:K.166, B:K.246, B:K.246, A:K.266 POP.26: 11 residues within 4Å: Chain C: H.15, D.17, D.239, R.245, K.246 Chain D: E.43, K.266 Ligands: MG.22, MG.23, K.25, PO4.35 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Water bridges: C:H.15, C:K.166, C:K.166, C:D.239, C:D.239, C:R.245, D:K.266, D:K.266 Salt bridges: C:H.15, C:K.246, D:K.266 POP.37: 10 residues within 4Å: Chain C: D.119, K.266, D.272 Chain D: H.15, D.17, K.166, K.246 Ligands: MG.24, MG.34, PO4.36 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.245 Water bridges: D:H.15, D:K.166, D:K.166, C:K.266, C:K.266, C:D.272 Salt bridges: D:H.15, D:K.166, D:K.246, D:K.246, C:K.266

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

EDO.6: 2 residues within 4Å: Chain A: A.110, P.112 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: N.71, R.74, E.75 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: E.75, K.154 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.147, E.354, R.363, H.365 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: G.362, R.363, E.364, H.365 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: S.81, D.82 Chain D: V.79, H.80, D.86, N.88 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.114, A.306, E.307, R.337 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: V.305, E.307, P.308, T.309 Chain B: K.222, F.224 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: K.209, P.210, I.211, L.212, P.213 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: R.39, V.40, A.41, E.56, I.57, T.58, K.270 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: D.82, M.83, R.162, Q.189, H.190, S.191, V.232 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: D.82, M.83, R.162, Q.189, H.190, S.191, V.232 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: E.130, K.177, I.178 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain C: E.13, Q.22, E.75, I.76, K.154, K.353 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain C: R.39, V.40, A.41, E.56, I.57, T.58, K.270 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain C: A.110, P.112 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: Y.281, M.344, P.367, K.370, D.372 Ligand excluded by PLIP

3 x K: POTASSIUM ION(Non-covalent)

K.16: 4 residues within 4Å: Chain A: E.43 Chain B: C.240 Ligands: MG.14, POP.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.43 K.17: 3 residues within 4Å: Chain A: D.239, C.240 Chain B: E.43 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.43 K.25: 4 residues within 4Å: Chain C: D.239, C.240 Chain D: E.43 Ligands: POP.26 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.43, H2O.23

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.33: 15 residues within 4Å: Chain D: L.122, M.123, F.124, I.248, T.251, Y.252, G.253, G.254, M.255, A.256, R.257, H.258, G.259, G.260, A.276 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:F.124, D:T.251, D:Y.252, D:G.254, D:A.256, D:G.259 Water bridges: D:A.256, C:H.258

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

2021-03-31

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosylmethionine synthase

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