SMTL ID : 6pbp.1

Pseudopaline Dehydrogenase with (S)-Pseudopaline Soaked 1 hour

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 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, 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, T.231, R.376, E.380 Ligands: O7J.2, EDO.3 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:T.170, A:T.170, A:E.380 Water bridges: A:G.33, A:A.36, A:R.60, A:R.60, A:R.376 Salt bridges: A:H.56, A:R.376, A:R.376 pi-Stacking: A:H.56 NAP.9: 26 residues within 4Å: Chain B: V.30, G.31, L.32, G.33, A.34, V.35, A.36, L.54, N.55, H.56, 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:H.56, B:R.60, B:T.170, B:T.170, B:R.376, B:E.380 Water bridges: B:G.33, B:A.36, B:R.60, B:R.60, B:R.60, B:A.114, B:S.116, B:S.116, B:S.116, B:R.376 Salt bridges: B:H.56, B:R.376, B:R.376 pi-Stacking: B:H.56, B:H.56

2 x O7J: N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid(Non-covalent)

O7J.2: 17 residues within 4Å: Chain A: A.169, K.184, K.187, V.230, T.231, V.234, H.235, Y.259, L.300, Y.305, R.335, Y.336, L.339, F.356, S.357, V.359 Ligands: NAP.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.259 Hydrogen bonds: A:T.231, A:Y.259, A:Y.259, A:Y.259, A:Y.305, A:Y.336 Water bridges: A:A.168, A:K.187, A:K.187, A:K.187, A:K.187 Salt bridges: A:K.184, A:K.187, A:H.235, A:R.335 pi-Stacking: A:Y.259, A:F.356 O7J.10: 17 residues within 4Å: Chain B: V.230, T.231, V.234, H.235, F.239, M.258, Y.259, L.300, N.304, Y.305, R.335, Y.336, L.339, F.356, S.357, V.359, V.377 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.259 Hydrogen bonds: B:Y.259, B:Y.259, B:Y.305, B:Y.336 Water bridges: B:N.304 Salt bridges: B:H.235, B:H.235, B:R.335 pi-Stacking: B:F.356

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

EDO.3: 8 residues within 4Å: Chain A: V.30, G.31, L.54, N.55, H.56, V.112, V.120 Ligands: NAP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.56 EDO.4: 8 residues within 4Å: Chain A: Y.191, R.228, P.293, 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:R.228, A:P.293 EDO.5: 7 residues within 4Å: Chain A: G.241, E.242, F.243, P.266, I.267, T.268, A.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.242, A:F.243, A:P.266 Water bridges: A:A.244 EDO.6: 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:R.277, A:R.277, A:E.329 Water bridges: A:G.270, A:A.274, A:R.276 EDO.7: 6 residues within 4Å: Chain A: W.279, C.280, S.283, R.287, P.293, A.321 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: H.308, P.343, F.344, S.345, H.353 Chain B: Y.262, P.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.343 EDO.11: 7 residues within 4Å: Chain B: G.241, E.242, F.243, P.266, I.267, T.268, A.271 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.242, B:E.242, B:E.242, B:F.243, B:P.266 Water bridges: B:A.244 EDO.12: 6 residues within 4Å: Chain B: A.114, D.115, F.141, R.383, K.384, L.387 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.115 Water bridges: B:D.115, B:K.384, B:L.387

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 Dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pseudopaline Dehydrogenase

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