SMTL ID : 6jil.1 (3 other biounits)

Crystal structure of D-cycloserine synthetase DcsG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 5 residues within 4Å: Chain A: W.45, F.69, R.72, V.73, V.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.45, A:F.69 Salt bridges: A:R.72 TLA.2: 11 residues within 4Å: Chain A: C.142, Y.143, K.202, R.220, R.254, E.269, E.271, S.276 Ligands: ADP.3, MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.143, A:R.254, A:E.271, A:S.276, A:S.276 Water bridges: A:K.202, A:K.202, A:R.220, A:R.254 Salt bridges: A:K.202, A:K.202, A:R.220, A:R.254, A:R.254

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 24 residues within 4Å: Chain A: K.92, I.106, V.135, K.137, G.141, C.142, Y.143, S.144, K.145, V.147, Q.175, P.176, Y.177, V.178, V.181, E.186, A.204, M.205, L.206, L.268, E.269 Ligands: TLA.2, MG.4, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.137, A:C.142, A:S.144, A:K.145, A:Q.175, A:V.178, A:E.186 Water bridges: A:K.92, A:K.92, A:G.141, A:Y.177, A:E.186, A:E.186, A:L.206 Salt bridges: A:K.92, A:K.92, A:K.137

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: K.202, D.256, E.269 Ligands: TLA.2, ADP.3, MG.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.269, H2O.1, H2O.2 MG.5: 5 residues within 4Å: Chain A: E.269, E.271 Ligands: TLA.2, ADP.3, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.269, A:E.269, A:E.271, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matoba, Y. et al., Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis. Febs J. (2020)

Release Date

2019-12-18

Peptides

Cycloserine biosynthesis protein DcsG: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cycloserine biosynthesis protein DcsG

Related Entries With Identical Sequence