SMTL ID : 6fbn.1

Human Methionine Adenosyltransferase II mutant (Q113A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 4 residues within 4Å: Chain A: D.78, Y.79, Q.80, V.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.78, A:Q.80 PEG.2: 4 residues within 4Å: Chain A: H.209, E.211, V.213, R.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.213

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

EDO.3: 2 residues within 4Å: Chain B: F.18, R.313 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.313 EDO.4: 3 residues within 4Å: Chain A: Q.256, G.257 Chain B: E.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.256 EDO.10: 2 residues within 4Å: Chain B: T.103, C.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.103 EDO.11: 8 residues within 4Å: Chain B: M.138, F.139, T.270, H.277, G.278, F.282, A.295, F.380 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.139, B:G.278 EDO.12: 4 residues within 4Å: Chain B: K.228, A.229, V.231, P.232 No protein-ligand interaction detected (PLIP)

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

SAM.5: 19 residues within 4Å: Chain A: A.55, E.70, D.116, I.117, G.133, D.134, K.289, I.322 Chain B: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, G.257, D.258 Ligands: PPK.6 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258, B:D.258, B:D.258 Water bridges: B:A.259, A:D.134, A:K.289, A:K.289 Salt bridges: B:D.258, A:D.134, A:K.289 pi-Stacking: B:F.250, B:F.250

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

PPK.6: 16 residues within 4Å: Chain A: D.134, G.279, G.280, A.281, K.285, D.291 Chain B: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: SAM.5, MG.7, MG.8, K.9 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.258, B:R.264, B:R.264, A:G.279, A:A.281, A:K.285, A:K.285 Water bridges: B:D.31, B:D.258 Salt bridges: B:H.29, B:K.181, B:K.265

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain B: E.23, K.181, K.265 Ligands: PPK.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.31, R.264 Ligands: PPK.6, K.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:D.31, H2O.2

1 x K: POTASSIUM ION(Non-covalent)

K.9: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: PPK.6, MG.8 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.57, B:D.258, B:A.259, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panmanee, J. et al., Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory beta subunit and quinolone-based compounds. Febs J. (2019)

Release Date

2019-01-30

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase isoform type-2