SMTL ID : 7p8m.1

Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with DMNB-SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.1: 11 residues within 4Å: Chain A: K.45, H.49, D.51, K.224, R.311 Chain B: D.82, Q.83, E.328, A.329, K.333 Ligands: MG.2 21 PLIP interactions: 8 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:A.329, A:R.311, A:R.311 Water bridges: B:N.80, B:N.80, B:D.82, B:Q.83, B:K.333, A:K.45, A:H.49, A:H.49, A:K.224, A:K.224 Salt bridges: B:K.333, B:K.333, A:K.45, A:K.45, A:K.45, A:H.49, A:K.224, A:R.311 3PO.4: 13 residues within 4Å: Chain A: D.82, E.328, A.329, K.333, H.338 Chain B: K.45, H.49, D.51, K.224, R.311 Ligands: MG.3, MG.5, 6IH.6 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.311, B:R.311, A:A.329 Water bridges: B:K.45, B:K.45, B:K.224, B:K.224, A:D.82, A:D.82, A:D.82, A:Q.83, A:H.338 Salt bridges: B:K.45, B:K.45, B:K.45, B:H.49, B:K.224, B:R.311, A:K.333, A:K.333, A:H.338

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.45, H.49, D.51, R.311 Chain B: Q.83 Ligands: 3PO.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.51, H2O.1, H2O.11 MG.3: 5 residues within 4Å: Chain A: E.328, K.333, H.338 Chain B: K.45 Ligands: 3PO.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.328, A:E.328, H2O.3 MG.5: 6 residues within 4Å: Chain A: Q.83 Chain B: K.45, H.49, D.51, R.311 Ligands: 3PO.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.51, H2O.10, H2O.11

1 x 6IH: 4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine(Non-covalent)

6IH.6: 24 residues within 4Å: Chain A: H.78, N.80, R.111, S.164, D.166, A.167, V.170, N.182, D.183, T.184, A.371 Chain B: H.49, P.50, D.222, K.224, A.239, N.282, A.284, Y.293, S.300, G.304, D.305, D.306 Ligands: 3PO.4 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:K.224, B:Y.293, B:G.304, B:D.305, B:D.305, A:N.80, A:D.166 Salt bridges: B:D.305, A:H.78, A:D.183 pi-Stacking: B:Y.293, B:Y.293 Hydrophobic interactions: A:A.167 Water bridges: A:R.111, A:S.164, A:S.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peters, A. et al., Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem (2022)

Release Date

2021-11-17

Peptides

S-adenosylmethionine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

S-adenosylmethionine synthase

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