SMTL ID : 1p7l.1

S-Adenosylmethionine synthetase complexed with AMPPNP and Met.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: D.238, C.239 Chain B: E.42 Ligands: MG.3, ANP.4 No protein-ligand interaction detected (PLIP) K.6: 5 residues within 4Å: Chain A: E.42, E.55 Chain B: D.238, C.239 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) K.11: 5 residues within 4Å: Chain C: D.238, C.239 Chain D: E.42 Ligands: MG.12, PPK.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.238 K.18: 4 residues within 4Å: Chain C: E.42 Chain D: D.238, C.239 Ligands: PPK.20 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.8, K.245 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.16, K.245 Ligands: K.1, ANP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.16 MG.7: 3 residues within 4Å: Chain B: E.8, K.245 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: D.16, R.244 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.16 MG.12: 4 residues within 4Å: Chain C: D.16, R.244 Ligands: K.11, PPK.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.16, C:D.16 MG.13: 4 residues within 4Å: Chain C: D.118, Q.119, D.271 Ligands: PPK.20 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.271 MG.17: 5 residues within 4Å: Chain C: K.165 Chain D: D.118, Q.119, D.271 Ligands: PPK.16 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain D: D.16, R.244 Ligands: PPK.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.16, D:D.16

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 25 residues within 4Å: Chain A: H.14, P.15, D.16, D.163, K.165, S.186, T.227, R.229, F.230, D.238, R.244, K.245 Chain B: D.101, I.102, D.118, G.259, G.260, A.261, K.265, D.271, I.302 Ligands: K.1, MG.2, MG.3, MET.9 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.163, A:S.186, A:T.227, A:D.238, A:D.238, A:R.244, A:R.244, B:D.118, B:G.259, B:A.261, B:K.265, B:K.265, B:D.271 Salt bridges: A:H.14, A:K.165, A:K.245 pi-Stacking: A:F.230, A:F.230 ANP.10: 25 residues within 4Å: Chain A: D.101, I.102, D.118, G.259, G.260, A.261, K.265, D.271, I.302 Chain B: H.14, P.15, D.16, D.163, K.165, S.186, T.227, R.229, F.230, D.238, R.244, K.245 Ligands: MET.5, K.6, MG.7, MG.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.163, B:S.186, B:T.227, B:T.227, B:D.238, B:R.244, B:R.244, B:K.245, A:G.259, A:A.261, A:K.265, A:K.265 Salt bridges: B:H.14, B:K.165, B:K.245 pi-Stacking: B:F.230, B:F.230

2 x MET: METHIONINE(Non-covalent)

MET.5: 10 residues within 4Å: Chain A: A.40, E.55, Q.98, I.102, G.117, D.118, K.269, I.302 Chain B: D.238 Ligands: ANP.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:G.237 Hydrogen bonds: A:E.55, A:Q.98 Salt bridges: A:K.269 MET.9: 10 residues within 4Å: Chain A: D.238 Chain B: A.40, E.55, Q.98, I.102, G.117, D.118, K.269, I.302 Ligands: ANP.4 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.55, B:Q.98, A:D.238 Water bridges: B:S.99, A:G.237 Salt bridges: B:K.269

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

SAM.14: 20 residues within 4Å: Chain C: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, I.232, D.238 Chain D: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302 Ligands: PPK.16 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:D.163, C:S.186, C:T.227, C:T.227, C:D.238, D:E.55, D:Q.98 Water bridges: C:T.227, C:R.229, D:S.99, D:D.101, D:K.269, D:K.269 Salt bridges: C:D.238, D:D.118, D:K.269 pi-Stacking: C:F.230, C:F.230 SAM.15: 20 residues within 4Å: Chain C: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302 Chain D: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, I.232, D.238 Ligands: PPK.20 19 PLIP interactions: 8 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:E.55, C:Q.98, D:D.163, D:S.186, D:T.227, D:D.238, D:D.238, D:D.238 Water bridges: C:S.99, C:I.102, C:K.269, C:K.269, D:T.227, D:T.227 Salt bridges: C:D.118, C:K.269, D:D.238 pi-Stacking: D:F.230, D:F.230

2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.16: 16 residues within 4Å: Chain C: H.14, D.16, K.165, D.238, R.244, K.245 Chain D: D.118, G.259, G.260, A.261, K.265, D.271 Ligands: K.11, MG.12, SAM.14, MG.17 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:R.244, C:R.244, C:K.245, D:G.259, D:A.261, D:K.265, D:K.265, D:K.265 Salt bridges: C:H.14, C:K.165, C:K.245 PPK.20: 16 residues within 4Å: Chain C: D.118, G.259, G.260, A.261, K.265, D.271 Chain D: H.14, D.16, K.165, D.238, R.244, K.245 Ligands: MG.13, SAM.15, K.18, MG.19 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:D.118, C:G.259, C:A.261, C:K.265, C:K.265, C:K.265, D:R.244, D:R.244, D:K.245 Salt bridges: D:H.14, D:K.165, D:K.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komoto, J. et al., Crystal structure of the s-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of s-adenosylmethionine synthesis from ATP and MET. Biochemistry (2004)

Release Date

2004-03-02

Peptides

S-adenosylmethionine synthetase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosylmethionine synthetase

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