SMTL ID : 7lnn.1

E. coli S-adenosyl methionine transferase co-crystallized with guanosine-5'-imidotriphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.114, E.307, R.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.337 EDO.2: 2 residues within 4Å: Chain A: F.223, F.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.223 EDO.3: 4 residues within 4Å: Chain A: Y.141, P.213, E.215, W.216 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain B: G.176, R.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.130, B:R.294, B:R.294 EDO.10: 3 residues within 4Å: Chain C: E.114, E.307, R.337 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.114, C:E.307, C:R.337 EDO.11: 2 residues within 4Å: Chain C: F.223, F.224 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.223 EDO.12: 4 residues within 4Å: Chain C: Y.141, P.213, E.215, W.216 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain D: G.176, R.294 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.130, D:R.294, D:R.294

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

PPK.4: 14 residues within 4Å: Chain A: E.9, H.15, D.17, K.166, D.239, R.245, K.246 Chain B: D.119, G.260, G.261, A.262, K.266, D.272 Ligands: MG.5 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.119, B:D.119, B:A.262, B:K.266, B:D.272, A:K.166, A:R.245 Salt bridges: A:H.15, A:K.166, A:K.246 PPK.8: 12 residues within 4Å: Chain A: D.119, G.260, G.261, A.262, K.266, D.272 Chain B: H.15, D.17, K.166, R.245, K.246 Ligands: MG.9 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.119, A:A.262, A:K.266, A:D.272, B:D.17, B:K.166, B:R.245, B:R.245, B:K.246 Salt bridges: B:H.15, B:K.166, B:K.246 PPK.13: 14 residues within 4Å: Chain C: E.9, H.15, D.17, K.166, D.239, R.245, K.246 Chain D: D.119, G.260, G.261, A.262, K.266, D.272 Ligands: MG.14 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:D.119, D:D.119, D:D.119, D:A.262, D:K.266, D:D.272, D:D.272, C:K.166, C:R.245 Salt bridges: C:H.15, C:K.166, C:K.246 PPK.17: 12 residues within 4Å: Chain C: D.119, G.260, G.261, A.262, K.266, D.272 Chain D: H.15, D.17, K.166, R.245, K.246 Ligands: MG.18 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.17, D:K.166, D:R.245, D:R.245, D:K.246, C:A.262, C:K.266, C:D.272 Salt bridges: D:H.15, D:K.166, D:K.246

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.17, K.246 Ligands: PPK.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, H2O.1, H2O.1, H2O.1 MG.9: 2 residues within 4Å: Chain B: D.17 Ligands: PPK.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.17, H2O.2 MG.14: 3 residues within 4Å: Chain C: D.17, K.246 Ligands: PPK.13 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.17, H2O.4, H2O.4, H2O.4 MG.18: 2 residues within 4Å: Chain D: D.17 Ligands: PPK.17 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.17, H2O.5

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

PO4.6: 3 residues within 4Å: Chain A: E.307, D.335, R.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.335 Salt bridges: A:R.337 PO4.15: 3 residues within 4Å: Chain C: E.307, D.335, R.337 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.335 Salt bridges: C:R.337

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
A

D
B

S-adenosylmethionine synthase

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