SMTL ID : 7cm9.1 (1 other biounit)

DMSP lyase DddX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: H.292, P.540, K.565, H.571, K.572, T.573, V.578, L.580, Q.606, E.607, M.608, V.609, E.614, G.635, I.636, N.708, P.709, L.720, D.721 Chain B: R.674 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.565, A:H.571, A:K.572, A:T.573, A:Q.606, A:V.609, A:E.614, A:I.636, A:N.708, A:D.721, A:D.721 Water bridges: A:G.635, A:N.708 Salt bridges: A:H.292, A:K.565, A:K.572, A:K.572, B:R.674, B:R.674 ATP.3: 21 residues within 4Å: Chain A: R.674 Chain B: H.292, V.563, K.565, A.570, H.571, K.572, T.573, V.578, L.580, Q.606, E.607, M.608, V.609, E.614, G.635, I.636, N.708, P.709, L.720, D.721 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.565, B:K.572, B:T.573, B:T.573, B:Q.606, B:V.609, B:E.614, B:I.636, B:N.708, B:D.721, B:D.721, A:R.674 Water bridges: B:E.706, B:D.721 Salt bridges: B:H.292, B:K.565, B:K.572, B:K.572, A:R.674

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: S.203, G.204, S.205, E.252 Chain B: S.345, G.346, G.347 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.346, B:G.347, A:G.204, A:S.205, A:S.205 SO4.4: 7 residues within 4Å: Chain A: S.345, G.346, G.347 Chain B: S.203, G.204, S.205, E.252 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.345, A:G.346, A:G.347, B:Q.202, B:G.204, B:S.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C.Y. et al., A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA. Elife (2021)

Release Date

2021-05-19

Peptides

DMSP lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DMSP lyase

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