SMTL ID : 6pbn.1

Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 residues within 4Å: Chain A: G.31, L.32, G.33, A.34, V.35, 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, T.231, R.376, E.380 Ligands: EDO.2, AKG.5, O77.6 26 PLIP interactions: 26 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.139, A:S.139, A:T.170, A:T.170, A:R.376, A:E.380 Water bridges: A:G.33, A:A.36, A:H.56, A:P.57, A:R.60, A:R.60, A:R.376, A:R.376 Salt bridges: A:H.56, A:R.376, A:R.376 pi-Stacking: A:H.56 NAP.7: 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, V.172, R.376, E.380 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:Y.166, B:Y.166 Hydrogen bonds: B:L.32, B:L.32, B:A.34, B:V.35, B:N.55, B:H.56, B:R.60, B:S.139, B:T.170, B:T.170, B:E.380 Water bridges: B:G.33, B:A.36, B:R.60, B:R.60, B:A.114, B:S.116, B:S.116, B:R.376, B:R.376, B:R.376, B:R.376 Salt bridges: B:H.56, B:R.376, B:R.376 pi-Stacking: B:H.56, B:H.56

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

EDO.2: 8 residues within 4Å: Chain A: V.30, G.31, L.54, N.55, H.56, V.112, V.120 Ligands: NAP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:H.56 EDO.3: 8 residues within 4Å: Chain A: Y.191, R.228, P.293, L.294, N.295, R.298, F.299, D.303 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.295, A:R.298 Water bridges: A:Y.191, A:R.228, A:P.293, A:D.303 EDO.4: 7 residues within 4Å: Chain A: P.269, G.270, G.273, R.276, R.277, E.329 Chain B: R.327 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.270, A:R.277, A:R.277, A:E.329 Water bridges: A:A.274, A:R.276 EDO.8: 8 residues within 4Å: Chain B: Y.191, R.228, P.293, L.294, N.295, R.298, F.299, D.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.295 Water bridges: B:R.228, B:R.298 EDO.9: 7 residues within 4Å: Chain B: P.346, A.347, D.348, R.352, H.353, F.354, D.355 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.348, B:R.352 Water bridges: B:F.354, B:F.354

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.5: 9 residues within 4Å: Chain A: T.231, H.235, F.239, M.258, Y.259, V.359, V.377 Ligands: NAP.1, O77.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.235 Water bridges: A:K.184 Salt bridges: A:K.184, A:H.235

1 x O77: N-[(3S)-3-amino-3-carboxypropyl]-L-histidine(Non-covalent)

O77.6: 15 residues within 4Å: Chain A: K.187, V.230, T.231, V.234, H.235, Y.259, L.300, R.335, Y.336, L.339, F.356, S.357, V.359 Ligands: NAP.1, AKG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.259 Hydrogen bonds: A:Y.259, A:Y.259 Water bridges: A:K.187, A:K.187 Salt bridges: A:K.187, A:R.335 pi-Stacking: A:Y.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. J.Biol.Chem. (2019)

Release Date

2019-10-30

Peptides

Pseudopaline Dehdyrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pseudopaline Dehdyrogenase

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