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

DsyB in complex with SAH and MTHB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: Y.129, F.133, Y.142, Q.146, S.150, G.173, G.174, G.175, F.179, D.196, F.197, V.200, G.222, D.223, A.224, S.239, Y.240, L.241 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.146 Hydrogen bonds: A:Q.146, A:S.150, A:D.223, A:D.223, A:A.224, A:S.239 Water bridges: A:Q.146 pi-Stacking: A:F.197 SAH.3: 17 residues within 4Å: Chain B: Y.129, F.133, Y.142, Q.146, S.150, G.173, G.174, G.175, F.179, D.196, F.197, G.222, D.223, A.224, S.239, Y.240, L.241 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.146, B:S.150, B:D.223, B:D.223, B:A.224, B:S.239 Water bridges: B:Q.146, B:G.174, B:G.177, B:F.179, B:S.239 pi-Stacking: B:F.197

2 x H9L: 4-methylsulfanyl-2-oxidanyl-butanoic acid(Non-covalent)

H9L.2: 9 residues within 4Å: Chain A: Y.97, Q.101, Y.142, Q.146, G.149, S.150, Y.240, W.287, H.291 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.240, A:Y.240 H9L.6: 7 residues within 4Å: Chain B: Y.97, Q.101, Y.142, Q.146, G.149, Y.240, W.287 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.240 Hydrogen bonds: B:Y.240

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: D.111 Chain B: D.103, R.104, Q.105, Y.107, G.108, L.109 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.105, B:G.108, B:L.109, A:D.111 TRS.5: 2 residues within 4Å: Chain A: G.50 Chain B: A.118 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.118, B:N.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C.Y. et al., Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB. Mlife (2022)

Release Date

2022-06-01

Peptides

DSYB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

DSYB

Related Entries With Identical Sequence