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

CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE SYNTHETASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: D.118, D.271 Chain C: H.14, D.16, K.165, K.245 Ligands: PO4.2, MG.3, MG.4 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.16 Salt bridges: C:H.14, C:K.165, C:K.245 PO4.2: 8 residues within 4Å: Chain A: A.261, K.265 Chain C: D.16, R.244, K.245 Ligands: PO4.1, MG.3, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.261 Salt bridges: A:K.265, C:R.244, C:K.245 PO4.7: 9 residues within 4Å: Chain B: D.118, D.271 Chain D: H.14, D.16, K.165, K.245 Ligands: PO4.8, MG.9, MG.10 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.16 Salt bridges: D:H.14, D:K.165, D:K.245 PO4.8: 8 residues within 4Å: Chain B: A.261, K.265 Chain D: D.16, R.244, K.245 Ligands: PO4.7, MG.9, MG.10 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: 9 residues within 4Å: Chain A: H.14, D.16, K.165, K.245 Chain C: D.118, D.271 Ligands: PO4.14, MG.15, MG.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.16, A:D.16, A:D.16 Salt bridges: A:H.14, A:K.165, A:K.245 PO4.14: 8 residues within 4Å: Chain A: D.16, R.244, K.245 Chain C: A.261, K.265 Ligands: PO4.13, MG.15, MG.16 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.261, A:D.16 Salt bridges: C:K.265, A:R.244, A:K.245 PO4.19: 9 residues within 4Å: Chain B: H.14, D.16, K.165, K.245 Chain D: D.118, D.271 Ligands: PO4.20, MG.21, MG.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.16, B:D.16 Salt bridges: B:H.14, B:K.165, B:K.245 PO4.20: 8 residues within 4Å: Chain B: D.16, R.244, K.245 Chain D: A.261, K.265 Ligands: PO4.19, MG.21, MG.22 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.3: 6 residues within 4Å: Chain A: D.118, Q.119, D.271 Chain C: K.165 Ligands: PO4.1, PO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.118, A:D.271 MG.4: 4 residues within 4Å: Chain C: D.16, R.244 Ligands: PO4.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain B: D.118, Q.119, D.271 Chain D: K.165 Ligands: PO4.7, PO4.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.118, B:D.271 MG.10: 4 residues within 4Å: Chain D: D.16, R.244 Ligands: PO4.7, PO4.8 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain A: K.165 Chain C: D.118, Q.119, D.271 Ligands: PO4.13, PO4.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.118, C:D.271 MG.16: 4 residues within 4Å: Chain A: D.16, R.244 Ligands: PO4.13, PO4.14 No protein-ligand interaction detected (PLIP) MG.21: 6 residues within 4Å: Chain B: K.165 Chain D: D.118, Q.119, D.271 Ligands: PO4.19, PO4.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.118, D:D.271 MG.22: 4 residues within 4Å: Chain B: D.16, R.244 Ligands: PO4.19, PO4.20 No protein-ligand interaction detected (PLIP)

8 x K: POTASSIUM ION(Non-covalent)

K.5: 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:E.42 K.6: 3 residues within 4Å: Chain A: G.243 Chain C: G.243 Ligands: K.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.243, A:G.243 K.11: 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:E.42 K.12: 3 residues within 4Å: Chain B: G.243 Chain D: G.243 Ligands: K.24 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:G.243, D:G.243 K.17: 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:E.42 K.18: 3 residues within 4Å: Chain A: G.243 Chain C: G.243 Ligands: K.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.243, A:G.243 K.23: 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:E.42 K.24: 3 residues within 4Å: Chain B: G.243 Chain D: G.243 Ligands: K.12 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:G.243, B:G.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takusagawa, F. et al., Crystal structure of S-adenosylmethionine synthetase. J.Biol.Chem. (1996)

Release Date

1996-03-08

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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