SMTL ID : 6gmz.1

Staphylopine dehydrogenase in complex with Histidine tag and citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

2 x ALA- HIS- HIS- ALA: ALA-HIS-HIS-ALA(Non-covalent)

ALA-HIS-HIS-ALA.1: 10 residues within 4Å: Chain A: Y.240, Y.286, I.320, F.335, D.336, F.337, A.339, V.340 Ligands: NH4.2, CIT.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.240, A:F.335, A:F.337, A:V.340 Hydrogen bonds: A:Y.286, A:Y.286, A:F.337 pi-Stacking: A:Y.240, A:Y.286 ALA-HIS-HIS-ALA.5: 10 residues within 4Å: Chain B: Y.240, Y.286, I.320, F.335, D.336, F.337, A.339, V.340 Ligands: NH4.6, CIT.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.240, B:F.335, B:F.337, B:V.340 Hydrogen bonds: B:Y.286, B:Y.286, B:F.337 pi-Stacking: B:Y.240, B:Y.286

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 6 residues within 4Å: Chain A: V.215, L.219, Y.240, Y.317 Ligands: ALA-HIS-HIS-ALA.1, CIT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.317 NH4.6: 6 residues within 4Å: Chain B: V.215, L.219, Y.240, Y.317 Ligands: ALA-HIS-HIS-ALA.5, CIT.7 No protein-ligand interaction detected (PLIP)

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 12 residues within 4Å: Chain A: K.168, S.211, S.212, H.216, Y.240, N.285, Y.286, R.316, Y.317 Ligands: ALA-HIS-HIS-ALA.1, ALA-HIS-HIS-ALA.1, NH4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.240, A:Y.240, A:N.285 Salt bridges: A:K.168, A:H.216, A:R.316 CIT.7: 12 residues within 4Å: Chain B: K.168, S.211, S.212, H.216, Y.240, N.285, Y.286, R.316, Y.317 Ligands: ALA-HIS-HIS-ALA.5, ALA-HIS-HIS-ALA.5, NH4.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.240, B:Y.240, B:N.285 Salt bridges: B:K.168, B:H.216, B:R.316

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain A: C.20, S.24, I.116, F.144, L.148, R.185, L.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.185 PG4.8: 7 residues within 4Å: Chain B: C.20, S.24, I.116, F.144, L.148, R.185, L.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hajjar, C. et al., Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis. J.Am.Chem.Soc. (2019)

Release Date

2019-04-10

Peptides

Staphylopine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Staphylopine dehydrogenase