SMTL ID : 6c4n.1

Pseudopaline dehydrogenase (PaODH) - NADP+ bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 24 residues within 4Å: Chain A: G.31, L.32, G.33, A.34, V.35, A.36, N.55, H.56, R.60, C.111, V.112, P.113, A.114, S.116, V.120, S.139, Y.166, A.168, A.169, T.170, K.171, T.231, R.376, E.380 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.166 Hydrogen bonds: A:L.32, A:L.32, A:A.34, A:V.35, A:N.55, A:R.60, A:A.114, A:S.116, A:S.139, A:T.170, A:T.170, A:E.380 Water bridges: A:G.33, A:A.36, A:H.56, A:R.60, A:R.60 Salt bridges: A:H.56 pi-Stacking: A:H.56 NAP.3: 26 residues within 4Å: Chain B: V.30, G.31, L.32, G.33, A.34, V.35, L.54, N.55, H.56, G.58, R.60, C.111, V.112, P.113, A.114, S.116, D.119, V.120, S.139, Y.166, A.168, A.169, T.170, K.171, R.376, E.380 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.166 Hydrogen bonds: B:L.32, B:A.34, B:V.35, B:N.55, B:H.56, B:H.56, B:R.60, B:A.114, B:T.170, B:T.170, B:E.380 Water bridges: B:G.33, B:A.36, B:R.60, B:R.60, B:D.119 Salt bridges: B:H.56 pi-Stacking: B:H.56, B:H.56

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: Y.191, R.228, L.294, N.295, R.298, F.299, D.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.295, A:R.298, A:R.298 Water bridges: A:Y.191, A:D.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J. Biol. Chem. (2018)

Release Date

2018-04-11

Peptides

Pseudopaline dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pseudopaline dehydrogenase

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