SMTL ID : 6h3f.1

Staphylopine dehydrogenase in complex with staphylopine and NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 21 residues within 4Å: Chain A: G.8, T.9, G.10, P.11, V.12, R.33, S.37, K.39, S.40, A.91, C.92, T.93, A.96, S.119, Y.147, G.149, D.150, T.151, R.357, E.361 Ligands: 8UX.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:T.9, A:G.10, A:V.12, A:R.33, A:S.37, A:S.40, A:S.40, A:D.95, A:S.119, A:G.149, A:D.150, A:T.151, A:R.357, A:R.357 Water bridges: A:T.9, A:T.9, A:A.13 Salt bridges: A:R.33, A:K.39, A:K.39, A:R.357, A:R.357 pi-Stacking: A:Y.147 pi-Cation interactions: A:R.33, A:R.33 NAP.5: 21 residues within 4Å: Chain B: G.8, T.9, G.10, P.11, V.12, R.33, S.37, K.39, S.40, A.91, C.92, T.93, A.96, S.119, Y.147, G.149, D.150, T.151, R.357, E.361 Ligands: 8UX.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.147 Hydrogen bonds: B:T.9, B:G.10, B:V.12, B:R.33, B:S.37, B:S.40, B:S.40, B:D.95, B:S.119, B:G.149, B:D.150, B:T.151, B:R.357, B:R.357 Water bridges: B:T.9, B:T.9, B:A.13 Salt bridges: B:R.33, B:K.39, B:K.39, B:R.357, B:R.357 pi-Stacking: B:Y.147 pi-Cation interactions: B:R.33, B:R.33

2 x 8UX: (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid(Non-covalent)

8UX.2: 4 residues within 4Å: Chain A: Y.240, Y.286, F.337 Ligands: NAP.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.168 pi-Stacking: A:Y.240 8UX.6: 4 residues within 4Å: Chain B: Y.240, Y.286, F.337 Ligands: NAP.5 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.168 pi-Stacking: B:Y.240

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.228, G.232, T.233, P.236, V.237, P.341, F.342, Q.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.228, A:T.233, A:V.237, A:V.237, A:F.342 GOL.7: 8 residues within 4Å: Chain B: A.228, G.232, T.233, P.236, V.237, P.341, F.342, Q.344 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.228, B:T.233, B:V.237, B:V.237, B:F.342

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

PG4.4: 5 residues within 4Å: Chain A: C.20, S.24, I.116, R.185, I.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.185 PG4.8: 5 residues within 4Å: Chain B: C.20, S.24, I.116, R.185, I.186 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

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