SMTL ID : 1mxb.2 (1 other biounit)

S-ADENOSYLMETHIONINE SYNTHETASE WITH ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 11 residues within 4Å: Chain A: G.259, G.260, A.261, K.265, D.271 Chain C: D.16, R.244, K.245 Ligands: MG.2, MG.3, ADP.6 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:R.244, C:K.245, A:K.265 Hydrogen bonds: A:A.261 PO4.7: 11 residues within 4Å: Chain B: G.259, G.260, A.261, K.265, D.271 Chain D: D.16, R.244, K.245 Ligands: MG.8, MG.9, ADP.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.261 Salt bridges: B:K.265, D:R.244, D:K.245 PO4.13: 11 residues within 4Å: Chain A: D.16, R.244, K.245 Chain C: G.259, G.260, A.261, K.265, D.271 Ligands: MG.14, MG.15, ADP.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Salt bridges: A:R.244, A:K.245, C:K.265 Hydrogen bonds: C:A.261 PO4.19: 11 residues within 4Å: Chain B: D.16, R.244, K.245 Chain D: G.259, G.260, A.261, K.265, D.271 Ligands: MG.20, MG.21, ADP.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Salt bridges: B:R.244, B:K.245, D:K.265 Hydrogen bonds: D:A.261

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.118, K.265, D.271 Ligands: PO4.1, ADP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.271, A:D.271 MG.3: 4 residues within 4Å: Chain C: D.16, R.244 Ligands: PO4.1, ADP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.16, C:D.16 MG.8: 5 residues within 4Å: Chain B: D.118, K.265, D.271 Ligands: PO4.7, ADP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.271, B:D.271 MG.9: 4 residues within 4Å: Chain D: D.16, R.244 Ligands: PO4.7, ADP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.16, D:D.16 MG.14: 5 residues within 4Å: Chain C: D.118, K.265, D.271 Ligands: PO4.13, ADP.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.271, C:D.271 MG.15: 4 residues within 4Å: Chain A: D.16, R.244 Ligands: PO4.13, ADP.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.16, A:D.16 MG.20: 5 residues within 4Å: Chain D: D.118, K.265, D.271 Ligands: PO4.19, ADP.24 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.271, D:D.271 MG.21: 4 residues within 4Å: Chain B: D.16, R.244 Ligands: PO4.19, ADP.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.16, B:D.16

8 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: E.42, T.242, S.263, K.265 Chain C: R.244 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:S.263 K.5: 5 residues within 4Å: Chain A: G.243, I.246 Chain C: G.243, I.246 Ligands: K.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.243, A:G.243 K.10: 5 residues within 4Å: Chain B: E.42, T.242, S.263, K.265 Chain D: R.244 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.42, B:S.263 K.11: 5 residues within 4Å: Chain B: G.243, I.246 Chain D: G.243, I.246 Ligands: K.23 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:G.243, B:G.243 K.16: 5 residues within 4Å: Chain A: R.244 Chain C: E.42, T.242, S.263, K.265 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.42, C:S.263 K.17: 5 residues within 4Å: Chain A: G.243, I.246 Chain C: G.243, I.246 Ligands: K.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.243, A:G.243 K.22: 5 residues within 4Å: Chain B: R.244 Chain D: E.42, T.242, S.263, K.265 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.42, D:S.263 K.23: 5 residues within 4Å: Chain B: G.243, I.246 Chain D: G.243, I.246 Ligands: K.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:G.243, D:G.243

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 20 residues within 4Å: Chain A: R.38, V.39, A.40, E.55, T.57, Q.98, D.118, K.265, K.269, D.271 Chain C: H.14, D.16, K.165, G.237, D.238, R.244, K.245 Ligands: PO4.1, MG.2, MG.3 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.98, A:Q.98, A:D.118, A:K.269 Salt bridges: A:K.265, C:H.14, C:K.165, C:K.245 ADP.12: 20 residues within 4Å: Chain B: R.38, V.39, A.40, E.55, T.57, Q.98, D.118, K.265, K.269, D.271 Chain D: H.14, D.16, K.165, G.237, D.238, R.244, K.245 Ligands: PO4.7, MG.8, MG.9 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.98, B:Q.98, B:D.118, B:K.269 Salt bridges: B:K.265, D:H.14, D:K.165, D:K.245 ADP.18: 20 residues within 4Å: Chain A: H.14, D.16, K.165, G.237, D.238, R.244, K.245 Chain C: R.38, V.39, A.40, E.55, T.57, Q.98, D.118, K.265, K.269, D.271 Ligands: PO4.13, MG.14, MG.15 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.98, C:Q.98, C:K.269 Salt bridges: C:K.265, A:H.14, A:K.165, A:K.245 ADP.24: 20 residues within 4Å: Chain B: H.14, D.16, K.165, G.237, D.238, R.244, K.245 Chain D: R.38, V.39, A.40, E.55, T.57, Q.98, D.118, K.265, K.269, D.271 Ligands: PO4.19, MG.20, MG.21 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:Q.98, D:Q.98, D:K.269 Salt bridges: D:K.265, B:H.14, B:K.165, B:K.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takusagawa, F. et al., Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution. Biochemistry (1996)

Release Date

1996-07-11

Peptides

S-ADENOSYLMETHIONINE SYNTHETASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-ADENOSYLMETHIONINE SYNTHETASE

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