SMTL ID : 7p84.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.1: 12 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, H.338 Ligands: MG.2 18 PLIP interactions: 8 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:A.329, B:H.338, A:R.311, A:R.311 Water bridges: B:D.82, B:Q.83, B:Q.83, B:K.333, A:H.49, A:H.49 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: 15 residues within 4Å: Chain A: D.82, D.183, M.327, 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, EU9.6 18 PLIP interactions: 11 interactions with chain B, 7 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, 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.2, H2O.2 MG.3: 4 residues within 4Å: Chain A: S.185, E.328 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.1 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.8, H2O.9

1 x EU9: [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium(Non-covalent)

EU9.6: 24 residues within 4Å: Chain A: H.78, N.80, R.111, S.164, D.166, A.167, V.170, N.182, D.183, H.338, 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 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:A.167 Hydrogen bonds: A:N.80, A:D.166, A:D.166, A:N.182, B:D.222, B:K.224, B:Y.293, B:G.304, B:D.305 Water bridges: A:S.164, B:D.306 Salt bridges: A:H.78, A:D.183, B:D.305 pi-Stacking: B:Y.293, B:Y.293

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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